One possible reason could be that he has been living a life apart from his family for so long that he feels alienated. He grew up alone in Konoha, with no knowledge of his family for a large part of his life. So, when suddenly faced with this family in the fanfiction, it's hard for him to accept.
One possible reason could be that the fanfiction portrays his family in a way that goes against his ideals. For example, if his family is depicted as being involved in immoral or unethical activities, Naruto, with his strong sense of justice, would have a hard time accepting them.
Naruto could be tired of the expectations placed on him. Everyone has always assumed he would be Hokage since he was a child. He might want to break free from those expectations and define his own path. He may feel that being Hokage is more about fulfilling others' wishes for him rather than his own true desires. So, he decides he doesn't want to be Hokage in this fanfiction.
One possible reason could be that Naruto has been mistreated by the villagers in Konoha for a long time. Despite his efforts to gain acceptance, if he's constantly faced with rejection or unfair treatment, it might lead to him not caring. For example, when he was a child, many villagers shunned him because he was the host of the Nine - Tails. This continuous negative experience could build up over time and cause him to lose his sense of loyalty to Konoha.
It could also be due to some family curse or prophecy. In the Naruto universe, there are often strange powers and curses. Maybe there was a prophecy that said Naruto's family had to keep their distance from him to protect him from some greater evil. So, they chose to neglect him in order to keep him safe, even if it was a difficult choice.
One possible reason could be that their personalities don't mesh well in the context of the fanfic. Naruto might be portrayed as someone who values different qualities in a partner that Hinata doesn't possess. For example, if the fanfic focuses on Naruto's love for adventure and freedom, he may see Hinata as too reserved and home - bound, which could lead to a lack of romantic feelings.
One possible reason is the way Naruto's character arc is perceived. Some might think his transformation from an outcast to a hero was too sudden or not well - developed enough. So in the fanfic, they feel he doesn't deserve the large fan base.
Maybe there are secrets in the family. For example, his parents might be involved in some dangerous and secretive missions that require them to keep their distance from Naruto to protect him, but Naruto misinterprets it as neglect.
One possible reason could be jealousy. If Naruto has the rare Mokuton ability, his family might be jealous of his potential power and neglect him out of spite.
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.
His non - acceptance might also attract the attention of enemies. If his family has some power or influence, the enemies might see Naruto's rejection as a weakness or an opportunity to create more chaos. So, it could drive the plot towards a more action - packed and dangerous direction as Naruto has to deal with external threats while also dealing with his family issues.