It could be due to some kind of misunderstanding. Perhaps Naruto saw his mother in a vision or something similar, and misinterpreted her actions. Say, he thought she was choosing something else over him, when in reality it was a sacrifice for his well - being.
One possible reason could be misinformation. Maybe in the fanfiction, Naruto was told false stories about his mother that made him dislike her. For example, if he was told she abandoned him for some untrue reason.
In this fanfiction, it might be that Naruto has some pent - up anger and he projects it onto his mother. Maybe he has had a tough life and he blames her for not being there, not realizing the circumstances that might have kept her away, like she could have been in a situation where she was forced to be away from him to protect him.
Perhaps there were some dark secrets in his clan that he discovers. These secrets could be related to past wrongdoings, like how they treated other clans or individuals. If Naruto has a strong sense of justice, learning about these things might make him hate his clan. It could also be that he feels ostracized or different within his clan, like if he has abilities or beliefs that are not accepted by the majority of the clan members.
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.
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.
Maybe in the fanfic, his sisters got some special powers or attention that Naruto felt was unfair. So he started to hate them out of envy.
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 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 misunderstanding. Maybe some false information was spread about his mother, making Naruto believe she had abandoned him. Another reason could be related to the secrecy around his mother. If he grew up feeling alone and not knowing about her, he might develop resentment.
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 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.