Perhaps in this fanfiction, her parents had some dark secrets. For example, they could be involved in some not - so - noble magic practices that she discovers later. This discovery might make her view them in a negative light and thus hate them. Also, if they had made some kind of deal that affected her life negatively, like her being used in some way, that would be a valid reason for her hatred.
One possible reason could be that in the fanfiction, her parents might have made a sacrifice that left her alone, and she resents them for not being there for her. Maybe she feels abandoned and that has led to her hatred.
It could be that in the story, her parents were very strict or controlling in a way that made her life miserable. Maybe they had very high expectations of her that she couldn't meet, or they were constantly comparing her to others. This constant pressure could have built up so much resentment in her that it turned into hatred.
Perhaps in this fanfiction, her parents have some secrets that Hermione discovers. These secrets could be related to the wizarding world and their connection to it. Their attempts to hide these things from her make her feel betrayed and thus lead to her hatred. For instance, if they knew about some dark magic in their family history but kept it from her.
One possible reason could be jealousy. Maybe she sees the Weasleys as getting things too easily in the wizarding world compared to her own hard - earned achievements. For example, they have a big family support system that she lacks, and she might envy that.
One possible reason could be that she discovers some dark secrets about the Cullens. Maybe she finds out they have been lying to her about their true nature in a more malicious way than in the original story. Another reason might be that she feels threatened by their vampire powers. If they accidentally or purposefully use their powers around her in a menacing way, it could make her feel scared and turn that fear into hatred.
One possible reason could be that he might feel abandoned. Growing up without them, he could resent the fact that they left him an orphan. He might think that if they were really so great, they would have found a way to survive and be there for him.
One possible reason could be a misunderstanding. Maybe Lupin did something that Harry misinterpreted as betrayal or negligence. For example, if Lupin was forced to keep a secret from Harry for his own safety, but Harry found out in a way that made him feel deceived.
Well, it completely flips the relationship dynamic. In the original, Harry had a longing for his parents who were taken from him. But in this fanfiction, the hatred changes the emotional core. It makes the character more bitter and less of the hero we know from the original, who was motivated by love for his parents.
One possible reason could be that fanfiction often takes creative liberties that may distort the complex character of Snape that J.K. Rowling created. Snape has a very intricate backstory and personality in the original series, and fanfiction might simplify or misinterpret it.
One possible reason could be that in the fanfic, the author might twist the story to make it seem like his parents' actions had unforeseen consequences that affected Harry negatively. For example, their fight against Voldemort led to Harry being an orphan and having to bear a great burden from a young age.
One possible reason could be the Ministry's corruption. In the original series, we saw some Ministry officials being more concerned with power and image than doing what was right. They often turned a blind eye to real threats like Voldemort's return in the beginning. So in the fanfiction, this corruption might be exacerbated, leading Harry to hate the Ministry.
One possible reason could be the lack of presence of his parents. Growing up without them, he might feel abandoned. And as for Konoha, if he hates it, it could be due to the way he was treated as an outcast, despite being the son of important figures. Maybe the villagers' coldness towards him made him resent the village that didn't seem to protect him from that.