One possible reason could be a misinterpretation of their relationships. Maybe the author wants to explore a different dynamic where Harry and Hermione bond over Ron's perceived flaws, like his occasional laziness or his insecurities that might come across as annoying to them in this fictional scenario.
Another reason might be to explore the characters in a more complex way. Harry and Hermione are both very intelligent and driven, and if they were to hate Ron, it could show how their values might be different from his. Maybe they start to dislike him because he doesn't share their level of academic or moral intensity, but this also allows for character growth as they might later realize the importance of his different perspective.
In some fanfiction, it could be due to a plot device to create drama. By having Harry and Hermione hate Ron, it can lead to all sorts of conflicts within the trio. For example, it might split their group and force them to choose sides, which can then drive the story in new and unexpected directions.
It's possible that Harry hates it because he has a certain image of Ron and Hermione in his mind. Fanfiction can sometimes create versions of them that are completely different from what he knows. For example, some fanfiction might focus on a love triangle that he doesn't think exists in their real relationship. This divergence from his perception could lead to his dislike.
Some people might just want to explore alternative scenarios for the sake of creativity. They may think it's interesting to see how the story would unfold if there was animosity between them.
Power could be a reason. If there's a chance for Ron and Hermione to gain a great deal of power by turning against Harry, some fanfictions might explore this. For instance, a new dark power might offer them something they've always desired, like the ability to reform the wizarding world in their own image. They might think Harry would oppose this, so they betray him to get what they want.
It could be that Harry has been influenced by some external force. In fanfiction, there could be a new dark wizard or a magical object that is affecting his mind. This new influence might make him think that Ron and Hermione are in danger if he stays close to them, so he ignores them to keep them safe.
Another possibility is that the fanfiction writer wants to explore a different side of their relationships. By having Hermione and Ron hurt Harry, it shows the complexity of human (or in this case, wizard) emotions. It could be a way to show that even the strongest friendships can have cracks and that mistakes can be made. It also allows for character development as Harry has to deal with this new situation, and Hermione and Ron may later realize their mistakes and try to make amends.
It might be due to cultural differences. Hermione comes from the wizarding world, and Annabeth from the demigod world. In fanfiction, these differences could be exaggerated, and Hermione might find Annabeth's 'alien' culture off - putting or difficult to understand, leading to dislike.
One reason could be a divergence from the original character traits. In the original story, Hermione and Ron have a complex relationship with love and friendship. Fanfiction that misrepresents Hermione's feelings towards Ron might go against the essence of her character. Maybe the fanfiction portrays her as hating Ron in a way that doesn't fit with her growth and development in the official series.
One reason could be envy. Hermione is often very good at academics and magic, and Harry and Ron might be envious of her success. For instance, if Hermione always gets top grades in potions class while Harry and Ron struggle, they could lash out at her out of frustration.
One reason could be jealousy. Maybe Ron feels that Harry is getting too close to Hermione and he's afraid of losing her attention. In fanfiction, authors often play with the characters' emotions. Harry, on the other hand, might see Ron as being too possessive of Hermione.
One possible reason could be social class differences. Hermione's parents are Muggles and might view Ron's large, wizarding family with some prejudice. They may see the Weasleys as a bit chaotic and irresponsible because of their financial situation.