Perhaps in this fanfiction, Naruto discovers some dark secrets about the village. Secrets that make him feel like he's been used all along. Like the village was only using him as a weapon against their enemies. This realization could make him resent everyone in the village, thus hating everyone.
Perhaps Naruto gets corrupted by some dark force. It changes his personality completely. He might start seeing all the people in the Hidden Leaf Village as the source of his problems. He could remember all the times he was ostracized as a child and now blames everyone for it. So in the fanfic, his hatred for everyone grows as he views the world in a new, darker light.
It could be Naruto himself. Since he hates everyone, his actions against the people he once cared about could make him the antagonist. He might start attacking the Hidden Leaf Village or other ninja villages, making him the main source of conflict.
Maybe a new, powerful and evil ninja from another land. This ninja could have come to the village and caused a lot of chaos, making Naruto believe that no one in his village was capable of protecting themselves or him. So he blames everyone for their weakness and starts to hate them all, with this new ninja being the root of the problem.
Well, in some RWBY fanfiction, the 'everyone hates Jaune' trope might be used to create drama. Maybe the author wants to explore how Jaune would grow and overcome such extreme dislike from others. It could also be a way to put him in difficult situations for character development.
Perhaps Harry has seen the worst in people too often. He might have witnessed so much greed, envy, and cruelty among those around him that he has lost all faith in humanity and thus hates everyone. He could be in a situation where he feels completely alone and that no one truly understands him.
Well, it could be that Percy has had some really bad experiences in his life that made him bitter towards everyone. Maybe he was betrayed by friends in the past, so now he just can't bring himself to trust or like anyone.
Well, this kind of fanfiction might be an interesting take on the character. It could explore a darker side of Harry Potter that we don't often see in the original series. Maybe the author wants to show how all the pressure and trauma he has endured could lead to a more cynical view of those around him.