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.
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 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 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.
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.
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.
Maybe Harry has had some really bad experiences that made him bitter towards everyone. For example, he could have been betrayed by his friends multiple times.