One reason could be that in this fanfiction's unique plot, there is a prophecy or some ancient magic that has been misinterpreted. This misinterpretation leads Harry to think that Muggle - borns are somehow linked to an impending doom for the wizarding world. So, as a result, he harbors hatred towards them. It could also be that there has been a series of unfortunate events that he wrongly blames on Muggle - borns, like a magical accident that he believes was caused by their 'uncontrolled' magic.
Well, in 'harry hates hermione fanfiction', it could be that the writer is trying to show how misunderstandings can lead to such extreme emotions. For example, perhaps there was a miscommunication about a spell or a magical event that made Harry wrongly think Hermione had betrayed him. Or it could be a way to explore how different personalities might clash more severely than shown in the original series, like Harry's impulsive nature conflicting more with Hermione's logical thinking.
Perhaps in the 'harry hates dunbledore fanfiction', Dumbledore is shown as being involved in some sort of secret plot that goes against Harry's values. For example, if Dumbledore was secretly working with the dark side in the fanfiction, Harry would naturally hate him. Also, it could be that Harry has discovered some long - hidden truth about Dumbledore that completely changes his view of him, like a past misdeed that Dumbledore has covered up.
Maybe in that fanfiction, McGonagall has some actions that Harry misinterprets. For example, she might be too strict with him in a way that he can't understand at that moment.
It could be due to a misunderstanding. In the fanfic, Remus might say or do something that Harry misinterprets as being against him. For example, Remus could be trying to protect Harry but his actions come across as controlling, which would make Harry dislike him and potentially hate him.
One possible reason could be that the 'light' in the fanfiction represents something he associates with strict rules or a false sense of goodness. Maybe it has been used to manipulate people, and Harry, being perceptive, sees through it and thus hates it.
Maybe in the fanfic, there could be a misunderstanding between them. For example, Ron might have accidentally broken Harry's trust in some way, like revealing a secret of Harry's that he wasn't supposed to.
Maybe in that fanfic, there are misunderstandings between Harry and the Weasleys. For example, they might have had an argument over something like magic use or family values that led Harry to dislike them.
In the original books, Harry is seen as a symbol of hope and acceptance. He fights against Voldemort who believes in pure - blood supremacy. But in the 'harry hates muggleborns fanfiction', Harry is on the wrong side of this equality issue. This fanfiction takes the character of Harry in a direction that is completely at odds with what we know from the original series. It also likely changes the relationships between characters. For example, his friendship with Hermione would not exist in the same way or might be completely broken in this fanfiction's universe.
In this fanfiction, perhaps there's some miscommunication. Maybe the Weasleys' boisterous nature is misconstrued by Harry. For example, their large family dynamic might be overwhelming to him at times, which could be a reason for the 'hate' in the fanfic.
One reason could be that in some fanfiction, the characterizations of Sasuke and Sakura might be off. Maybe Sasuke is portrayed as overly cruel to Sakura in a way that doesn't seem true to his character in the original series. Another reason could be that the storylines in these fanfictions are too clichéd, like always having Sasuke constantly reject Sakura in the same uninteresting ways.