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.
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, 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.
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.
One possible reason could be a sense of betrayal. Maybe he felt abandoned or mistreated by Konoha in some way. For example, if he was shunned because of the power within him that others feared.
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.
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.
Perhaps in the fanfiction, Dark Naruto has been betrayed. It could be that someone he trusted deeply, like a mentor or a close friend, turned on him. This act of betrayal could make him lose faith in humanity and lead to his hatred for everyone. He might think that if one person can betray him, then anyone can, so he hates them all without distinction.
One possible reason could be that Dark Naruto might see Kushina as a symbol of the world that rejected him. Since she was an important part of Naruto's family and the village, and Dark Naruto represents Naruto's negative emotions, he could resent her for the life he didn't have. He may feel that if Kushina had been there for him more (in his twisted view), he wouldn't have turned into this dark version.