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.
Maybe in this fanfiction, the village elders or some powerful ninja within the village made decisions that deeply affected Naruto in a negative way. For example, they could have withheld important information from him about his parents or his own powers, making him feel betrayed and thus leading to hatred. Also, if the village failed to protect his loved ones, like if they were killed due to the village's actions or inactions, that would be a strong reason for Naruto to hate the village.
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 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 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 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 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.
One possible reason could be feeling betrayed by the village's secrets and politics. Maybe he discovers some dark underbelly of the Leaf Village that makes him lose faith in it.
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.
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.
One possible reason could be a misunderstanding. Maybe some false information was spread about Kushina that made Naruto believe she had wronged him in some way. And for his sister, perhaps there was some sort of jealousy or miscommunication. For example, if his sister got more attention from their father or something similar.
Perhaps they have wronged Naruto in some way in the fanfiction. They could have betrayed him, like telling his secrets to others or getting him into trouble on purpose. This would lead to Naruto developing hatred towards them.