One possible reason could be a divergence in values. Maybe in this fanfiction, Naruto's family holds values that are completely opposite to what Naruto believes in. For example, if his family is shown to be more focused on power and status within the Justice League world, while Naruto values friendship and helping the weak.
Another reason could be neglect. If Naruto's family is always occupied with their own affairs in the Justice League, like fighting big villains or political power plays, and they have no time for Naruto, it could lead to his hatred. They might not have been there for him during his formative years or important events in his life.
It could also be due to some external influence. Perhaps an enemy manipulated Naruto's mind in the fanfiction, making him see his family in a negative light. This enemy might have used some form of mind - control or false memories to turn Naruto against his family.
One possible reason could be feeling neglected. Maybe his family was always preoccupied with other matters, like protecting the village, and didn't give him enough attention. So he grew to resent them.
One possible reason could be that he feels neglected. Maybe his family was always too busy with other things and didn't give him enough attention. This lack of attention during his formative years could have led to feelings of resentment.
One possible reason could be a misunderstanding within the family. Maybe there were secrets kept from him that made him feel betrayed. As for Konoha, perhaps he felt ostracized or not fully accepted by the village despite his efforts, which led to his hatred.
One possible reason could be that in the fanfiction's unique take, Naruto's family might have abandoned him in a cruel way. Maybe they left him alone in a dangerous situation which made him feel betrayed and thus led to his hatred.
One possible reason could be misinformation. Maybe in the fanfiction, Naruto was told false stories about his mother that made him dislike her. For example, if he was told she abandoned him for some untrue reason.
Perhaps there were some dark secrets in his clan that he discovers. These secrets could be related to past wrongdoings, like how they treated other clans or individuals. If Naruto has a strong sense of justice, learning about these things might make him hate his clan. It could also be that he feels ostracized or different within his clan, like if he has abilities or beliefs that are not accepted by the majority of the clan members.
It could be due to a misunderstanding. Perhaps there was an incident where his sister was involved, but Naruto misinterpreted her actions as something malicious against him. Like she might have accidentally broken something precious of his and he thought it was on purpose.
Maybe in the fanfic, his sisters got some special powers or attention that Naruto felt was unfair. So he started to hate them out of envy.
One possible reason could be a misinformation or false memories planted in Naruto's mind. Maybe some enemy with mind - control abilities made Naruto believe that his mother had done something unforgivable. Another reason might be a misunderstanding about her actions in the past. For example, if Naruto thought his mother sacrificed something important for a reason he didn't understand at first, he could misinterpret it as a wrong choice and develop hatred.