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.
One reason could be the alteration of McGonagall's personality. If in fanfiction she is made to be overly strict or mean, Harry, who knows her real character, would dislike this new version. In the original series, McGonagall was strict but fair, and any deviation from that in fanfiction might be off - putting to Harry.
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.
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.
It could also be due to some actions of McGonagall that seemed suspicious to Harry. Perhaps she made a decision regarding Hogwarts or Harry's safety that Harry didn't fully understand at the time. In the complex world of the wizarding school, decisions are often made with many factors in mind, but Harry might not be aware of all of them, leading to his distrust.
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.
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.
One possible reason could be that she is under some sort of dark magic influence. Maybe a spell has been cast on her that makes her act out of character and abandon Harry.
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.
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.