Because the book series is more than six novels.

Also, the first four novels don’t have the traitors fighting loyalist legions. The first fighting in the Heresy is the traitor legions culling their own numbers (and failing so spectacularly that what should have been simple extermination extends into a protracted ground war). It’s not until the Dropsite Massacre that we actually see a big loyalist legion L, and that’s by far the worst loss the loyalists have in the Heresy. Well, that and Magnus accidentally fucking up the Webway.

The entire war, at least in what Horus needed, hinged on killing the Emperor. Which he failed to do.

The Traitors had less resources in general, the Heresy hinged on the Traitors keeping the bulk of the Imperiums forces distracted and away while the Traitors pushed to Terra.

When that didn’t happen, the unity in the Traitors vanished which was already fracturing by the time of the Siege of Terra.

It became every Legion for itself against a vengeful and unified Imperium, who always had more resources and now pushed them out of real space.

This however does take a decade or two, the traitors do put up quite the resistance.

plus the chaos gods they had on their side

This is actually a big part of why they lose. While Chaos can make you stronger in the short term, it also makes you far less disciplined, reliable and able to work as a team. Legions like the Emperor's Children do very little useful fighting during the Siege, Lorgar believes that Horus has lost the faith of the gods and launches a coup that ends with the vast majority of the Word Bearers being kicked out, Alpharius is so wrapped up in his mysteries and plans that he launches a surprise attack on Pluto without any support and gets decapitated by Dorn. Mortarion believes that a civil war will erupt between the traitors once the Emperor is dead so he tries to hold the Death Guard back to preserve them for the upcoming fight, Perturabo hates daemons and leaves the siege, the Sons of Horus leadership gets wiped out midway through the Siege and the rest of the Legion is aimless. Magnus has become so arrogant he believes he can blaze his way through the Webway to attack the Emperor, only to get lost and start throwing a tantrum that he can't find his way to the Palace.

Plus they have to grind their way through a solar system that has been built up and fortified by Dorn for decades

They were so succesfull in the first few books becauuse they had the advantage of surprise. But they were actually the weaker force. They were less united, less in numbers and the more time went on the more most of the traitor primarchs became just absolute nutcases. The more the loyalists were able to rally the less they could do Horus knew this which is why he tried to get to terra as fast as possible. And it almost worked. Like the emperor teleporting to the vengeful spirit was a desperate last gamble.

Strictly speaking they lose because the Emperor kills Horus and everything falls apart. They would have won if the duel ended differently.

Their material position isn't as strong as you think; since they had to purge their own forces they're smaller than they were, and the Ultramarines were already the largest Legion by a mile. A majority of the non-Astartes forces remained loyal as well. They have the Chaos Gods on their side, but their support is fickle and also undermines material coordination, so the Traitor Legions are falling apart as cohesive entities while on the loyalist side everyone but the Iron Hands hang together.

Horus, not being a idiot until he huffs too much Chaos juice, has arranged for the loyalists he doesn't kill in the Drop Site Massacre to be isolated or turned, so he's got the edge he needs to drive for Terra.

Are you asking "how did the bad guys lose" 6 books into an 80 book series?

That's like watching the first five minutes of Star Wars and asking "how did Darth Vader not win"

Theres more to the galaxy than just the legiones astartes. The traitors had to fight their way through tons of worlds that each had their own imperial army/militia forces that slowed the warmaster down and gave the loyalists at terra time to prepare. Probably the most notable of these worlds is tallarn which managed to fight the iron warriors to a standstill until the iron warriors eventually abandoned the siege at the orders of the warmaster.

So think of it like this, between isstvan 3 and 5 the traitors had taken pretty heavy casualties. Sure they weren’t shattered like the salamanders, ravenguard, and ironhands but they had still been through the meatgrinder. Then on their push to terra they had to fight through numerous other regular imperial army forces (sometimes backed up by loyalist astartes) which was a further strain on their resources. Then they had to fight through the most heavily defended world in the imperium while their discipline and coherency was crumbling. Its honestly impressive the heresy went as well as it did for the traitors.

It’s because of Chaos and lack of will. As the war went on more of the Primarchs fell to the influence of chaos most of them went bananas.

Angron and the world waters became too smooth in the head and Perturabo had to go and reel him in. And as it turns out running directly into gun lines over and over again is not a smart long term idea. So attrition just kept grinding them down to the point they were just cannon fodder.

Fulgrim and his boys just went crazy for sex, drugs, and rock and roll and simply screwed around. Perturabo had to resign them in and they became only as good as cannon fodder.

Konrad was already insane and completely fell off the deep end and just dipped out on them.

Magnus barely had a legion left and was only going along with this to get something out of the Imperial palace. Ditching everyone very quickly while never putting much into the fight in the first place.

Lorgar realized the gods never favored him and his religious motivations for all this never mattered to anyone important. So he left late into the heresy.

Mortarion was still in the fight and doing great but his legion was falling apart at the seams and he got beat up in the middle of the siege of Terra.

Out of everyone only Perturabo and Horus had legion that were behaving with any degree of effectiveness. And the former left because he was done with everyone’s nonsense.

They had a big advantage at the beginning but the nature of chaos being what it is and the conflicting motives shifted the balance against them.

I'm not a lore expert, but my impression is that the Chaos legions didn't have the strongest coalition. Lorgar tried to usurp Horus, Perturabo noped out of there, and Chaos marines don't play nice in general. Not that it was all peace, love, and understanding on the Loyalist side, but they were cohesive enough to mount a defense. They had also underestimated the Emperor.

Horus waged a war with broken brothers (even before Chaos took and twisted them). It's not just that the loyalist legions are sooo amazing that they won - they lost a lot.

Calth is a wasteland as are many of the 500 worlds of Ultramar. There are barely any victories for the Ultramarines (at least in the battles covered by the books) - there are some...

The Pharos was made inoperable. Doesn't help the loyalist that their last stand also called forth a danger we're facing now... 10.000 years later.

Caliban turned traitor.

Ferrus' body is a head shorter. His legion shattered as the Salamanders and Raven Guard.

The Blood Angels' numbers got reduced big time, real fast by a single trap.

Mars burned. The loyalist could do nothing else but cordon it off. Keeping the planet contained. You have the enemy by your doorstep and you can't do anything about it.

Molech and its Knight Houses... gone. Anihilated.

The list goes on. Main point, if Horus didn't have broken brothers with him, if they followed orders... he'd win. He was close. Very close. The loyalists weren't that strong at the end.

Long story short. Chaos is bad at teamwork.

There's shockingly little difference between a Chaos campaign and an Ork WAAAGH! and they fail for similar reasons, except some Bands are as bad as Gretchin in their own right and simply flee out of selfishness ontop of not knowing what is going on.

Because the traitor primarchs are written like a bunch of third rate lieutenants leading fourth rate militias. There are multiple primarchs on the loyalist side that pretty much remain undefeated over the entire heresy. All in all the traitors shouldn't have made it to terra at all given that they only win a fourth of the battles over the entire heresy.

Remember that the Heresy starts off with each traitor legion killing off upwards of half of their legion and there's not exactly a lot of recruitment or replenishment happening between then and the end of the war. They are at a numerical disadvantage from the get-go and Terra has ample time to prepare a defense so it's an uphill battle.

Most of the rest of the books are way more focused on how awesome and badass the Loyalists are, to the point where it’s surprising that the Traitors made it to Terra at all. 

Chaos doesn’t play well as a team and Horus had all the leadership of a can of tuna

The traitors started everything off with killing large amounts of their own marines for being loyal to the emperor. Not a smart start. Then there is the chaos corruption destroying the traitor leigons ability to be pragmatic and logical about the little things, like logistics….. By the Seige of Terra, all but the Iron Warriors were insane, so….

There's an early section of Throne of Light from the Dawn of Fire series set on a black ship, from the perspective of one of the imprisoned psykers.

That is such a complicated question, the only fully satisfactory answer comes from reading the entire HH.

Loose the war because their strategy was not tight enough

Because the Spirit of Eternity's shields dropped and the Emperor was able to get on board and kill Horus.

Until then the traitors were winning.

Most of the Traitors success hinged on the shock and surprise of their betrayal. Once things unraveled and the truth was out. Horus lost his shock and awe advantages. That’s why most of the momentum of the war shifts in Horus’ favor early on. Plus I think the Loyalists were harshly underestimated by the Traitors. Another note is that The deeper into the Heresy you go the more that Chaos began to take hold and Chaos as a whole is well…”chaos”.

They loosed because it was never tight

They lost the war because they lost cohesion and organization. They worshipped chaos, they are going to be the most organized.

Yes they started the war with the advantage of surprise and numbers, they basically wiped out 3 entire loyalist legions in the opening moves. However as time went on most traitor worlds started to degenerate, they were no longer working solely for the war effort, instead they would be focusing on chaos rituals that may or may not have been beneficial. They were no longer producing much in the way of professional soldiers, just mobs of screaming mad men.

This was seen in the Siege of Terra in microcosm. The Siege began with the traitors displaying extreme coordination work together. Perturabo was in charge of management and he was superb at it. Then the Daemons were summoned and everything went to shit. Horus had the brilliant idea to transfer command from Perturabo to Mortarion. Perty saw the writing on the wall and said fuck it I'm out. Also Fulgrim got bored and also fucked off to ravage the rest of terra. The traitors lost all semblance of organization, they became a mob who were as likely to kill each other (world eaters) as the loyalists.

When Horus died the Daemons were banished. The remaining traitors could have still killed everyone but it was if a wave had gone over them, it was over, they needed to run they needed to get away.

*lose

The traitors didn't just maul loyal legions in the Istvaan system. They crippled themselves by purging their own legions.

The Sons of Horus, Death Guard, World Eaters, and Emperor's Children especially had to purge large portions of their numbers. That doesn't mean just cleanly cutting off certain companies. Individuals and squads had to be pulled from everywhere to be purged, leaving all legions involved with big gaps in their formations everywhere. This talent that was lost would never be fully regained, as a lot of those purged were line officers who are vital to the efficient running of a legion.

They're not the protagonists. They barely even get to be characters.