It could also be that Naruto has been influenced by some external force in the fanfiction. For instance, an enemy might have planted false memories or ideas in his head, making him believe that his parents and sister are bad. This false perception could then fuel his hatred.
Communication is key. Naruto and his sister could sit down and have an honest conversation about what's bothering him. They could clear up any misunderstandings that led to his hatred.
The story could develop with Naruto leaving Konoha to find his own path. He might seek out other ninja villages or hidden places to train and become stronger on his own terms, away from the place and the family ties that he resents.
The story could end with Naruto realizing his hatred was misdirected. After some big event or revelation, he discovers that his brother and sister actually care for him deeply. They all reconcile and become a closer - knit family.
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 common plot could be that the sister has a different ideology. For instance, she might believe in a more radical approach to achieving peace in the ninja world compared to Naruto's more inclusive and forgiving way. This difference could lead to clashes and eventually Naruto's hatred. Another plot could be a power struggle. If the sister is extremely powerful and uses her power in a way Naruto doesn't approve of, like being cruel to weaker ninjas, it could make Naruto hate her.
He could hate them because he felt they were absent during his difficult childhood. Naruto faced a lot of loneliness and bullying, and if he thought his parents could have prevented it but didn't, that would breed hatred.
One possible reason could be jealousy. Maybe the sister is more favored by the villagers or has some special abilities that Naruto feels overshadow his own. This could lead to a sense of envy and ultimately hatred.
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.