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.
It could also be that there were secrets in the family that he discovered. For example, if he found out that his family had some sort of dark past or made some unforgivable decisions that affected him or others. This realization might have made him turn against them with 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.
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 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 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 that Naruto feels abandoned. His father was not around during his childhood, and he had to face a lot of hardships alone. Growing up without a father figure, he might have developed resentment.
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.
One possible reason could be the way he was treated as a child. He was ostracized and shunned by many villagers because of the Nine - Tails inside him. This constant rejection and coldness from the people around him might have led to his hatred in the fanfiction.
One possible reason could be the lack of presence of his parents. Growing up without them, he might feel abandoned. And as for Konoha, if he hates it, it could be due to the way he was treated as an outcast, despite being the son of important figures. Maybe the villagers' coldness towards him made him resent the village that didn't seem to protect him from that.
One possible reason could be a misunderstanding. Maybe his team made a decision without consulting him, which made him feel left out and thus led to hatred. For example, if they took on a mission without him, Naruto, who values being part of the team, might feel betrayed.
It could also be due to differences in values. If Dark Naruto had different beliefs about power, friendship, or loyalty compared to his family, and they constantly clashed over these, it might lead to his hatred. For instance, if his family adhered strictly to Konoha's traditional values but he saw them as restrictive.