It could also be due to a lack of support. Naruto was constantly in trouble and trying to prove himself. If his family didn't show up in any way to support him and Konoha didn't do enough to encourage him in a positive way, but rather just punished him for his pranks, he might grow to hate them both.
One possible reason could be jealousy. Maybe Naruto has some special abilities or a prophecy surrounding him that makes his family members, who might be less favored, jealous. For example, if there's a prophecy that Naruto will be the most powerful ninja in the village, his siblings or parents might envy that future for him and start to hate him out of their own insecurities.
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.
Another reason could be that he witnesses corruption or unfairness within the village leadership. If he sees that the system is rigged against certain groups, including himself or his friends, he could grow to hate Konoha and decide to leave.
Perhaps she discovers some dark secrets about Konoha's past. Things like the way the village treated certain clans or individuals unfairly. If she uncovers that Konoha was involved in some unethical actions in the past, it could make her lose faith in and start to hate the village. Also, if her loved ones were wrongly treated or sacrificed by Konoha's decisions, that would be a strong reason.
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.
There could also be political reasons. Some factions within Konoha might have seen Naruto as a tool or a threat to their own political power. His influence and popularity could have disrupted the existing power balance, leading to animosity from those who wanted to maintain the status quo.
One possible reason could be that he discovers some long - hidden family secrets that make him feel betrayed. For example, if he finds out that his family was involved in something unethical in the past. Another reason might be that he feels constantly overshadowed by his family's legacy and can't form his own identity within the family, so he decides to leave to find himself.
Maybe in this fanfic, the author wants to create a unique and dark plot. Kushina might be made to hate Naruto due to some kind of misunderstanding. For example, she could be misled to believe that Naruto has some connection to a great evil that she is against.
A possible reason could be jealousy. If Naruto had a sibling who was always favored by their parents, he might grow to hate his family. He would feel like he was always in the shadow of his sibling and that his family didn't care about him as much.