Maybe he has some deep - seated insecurities. He might worry that he won't be able to live up to the expectations of his family. Naruto has always been striving to prove himself to others, and with a family, there would be new sets of expectations that he may not feel confident in meeting. Also, he could be worried about the family getting hurt because of his dangerous life as a ninja.
One possible reason could be that Naruto is so used to being on his own and having his own independent life. He has grown up without a traditional family for a long time, and the idea of suddenly having a family might seem very foreign and restrictive to him. He might fear losing his freedom and the self - made identity he has created over the years.
One possible reason could be that in the fanfiction, his family might have been portrayed as overly strict or controlling. Maybe they forced him into a certain path he didn't want to take, like a particular ninja training regime that Naruto found too rigid.
One possible reason could be a long - held misunderstanding. Maybe Naruto discovers some family secrets that he misinterprets as betrayal or neglect. For example, if he finds out that his family had made some sort of pact that he disagrees with, it could lead to his rejection.
One possible reason could be that he has some unresolved issues from his past, like the absence of his parents during his childhood which made him feel a sense of detachment. Maybe he is so focused on achieving his ninja goals that he unconsciously starts to ignore his family. Another reason might be some sort of miscommunication within the family. For example, if there are secrets that the family has been keeping from him, he might feel betrayed and thus choose to ignore them.
It could also be due to some sort of mind - control or curse. In the Naruto universe, there are many powerful jutsus and dark magics. Perhaps an enemy has cast a spell on him that makes him not care about his own life. This would be a dangerous situation as he could be easily manipulated into dangerous situations without self - preservation.
One possible reason could be that Naruto has grown so much on his own journey. He has faced numerous challenges and made many friends who have become like family to him. So, in a sense, he feels self - sufficient and no longer feels the acute need for his absent parents.
One possible reason could be a misdirection in his goals. If in the fanfiction he is overly focused on proving himself to the village, he might think that family is a distraction. So, he starts to distance himself from his family to concentrate more on getting recognition from the village.
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.
It could be due to miscommunication. In the fanfiction, perhaps there were misunderstandings within the family. For example, Naruto might have overheard something that made him think his family didn't have his best interests at heart, but in reality, it was all a big mix - up. So, he gradually lost trust in them.
One possible reason could be a divergence in values. Maybe in the fanfiction, Naruto discovers that his family was involved in some dark or unethical deeds that go against his principles. For example, if his family was secretly working with an enemy organization that Naruto has been fighting against. Another reason might be a sense of betrayal. If his family had made decisions in the past that put Naruto in a difficult or dangerous position without his knowledge, he could feel the need to denounce them. Also, it could be due to a misunderstanding. False information might be spread about his family, leading Naruto to believe they are not what he thought they were.
In some fanfictions, Naruto might abandon his family due to a false prophecy that convinces him he's a danger to them. He may think that by leaving, he can protect them from harm that might come his way because of his past or enemies.