Perhaps he blames the village for not protecting his loved ones well. For example, if something bad happened to Iruka or other important people to him due to the village's negligence. He might grow to hate it. Also, if he feels that the village has always treated him as an outcast, more than just because of the Nine - Tails inside him, but in terms of real opportunities and acceptance, that could fuel his hatred.
It could be that the village's treatment of other marginalized groups makes Naruto angry. If he sees that the village is unjust towards certain clans or individuals, and doesn't do enough to correct it, he might start to hate the place that is supposed to represent justice and peace.
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 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 a misunderstanding. Maybe some false information was spread about Kushina that made Naruto believe she was a bad person. For example, if there were rumors that she abandoned him for some untrue reason, it might lead to his hatred.
It could be that Yugao has a connection to an enemy or a group that Naruto dislikes. This connection could make Naruto view her with suspicion and ultimately hatred. In some fanfiction scenarios, she could be unknowingly involved with a plot against Naruto or his village.
It could also be related to personal relationships. Tsunade might have been hard on Naruto in a way that he felt was unjust. Perhaps she was overly critical of his unorthodox ninja techniques or his impulsive nature, and over time, this built up into hatred. Naruto, being someone who values respect and recognition, could have resented her for not seeing his potential in the way he wanted.
One possible reason could be the pressure associated with the Hokage title. Naruto has always been in the spotlight and being Hokage comes with a huge burden of responsibility. Maybe in the fanfiction, he resents how it restricts his freedom to just be himself and have adventures like he used to.
One possible reason could be that he feels burdened by the expectations associated with the Uzumaki clan. Maybe he doesn't like the constant attention or the pressure to live up to the clan's legacy.
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.
One possible reason could be a misunderstanding. Maybe Naruto misinterprets some of Sasuke and Sakura's actions as being against him or the village. For example, Sasuke's quest for power might seem like a threat to Naruto, and he could misread Sakura's loyalty to Sasuke as a form of betrayal to their friendship.
Maybe his sister is always favored by their parents, making Naruto feel left out and thus develop hatred.
One possible reason could be the way the villagers treated him as a child. They ostracized him because he was the host of the Nine - Tails. He was often alone and looked at with fear and disdain, which could have gradually built up his hatred.