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.
Perhaps in the fanfiction, Naruto accepts his dark emotions with the help of his friends. His friends, like Sasuke, Sakura, and Kakashi, might encourage him to face his inner demons. They tell him that it's okay to have dark emotions and that everyone has them. Naruto then starts to accept his own, knowing that he doesn't have to face them alone. His friends' support gives him the confidence to embrace his whole self, including the darker aspects of his emotions.
One possible reason could be that his newfound 'godlike' powers make his family feel estranged. They might not understand his sudden transformation and the magnitude of his power, which creates a sense of fear or discomfort, leading them to ignore him.
He could also distance himself from them. Naruto might choose to avoid his family, not wanting to be around them as a way to show his anger. He could move out or stop participating in family activities.
It could also be that his siblings continuously rejected him and his ideals in the past. Naruto has always strived for peace and acceptance, and if his siblings constantly opposed him on these fundamental things, it might lead to his unwillingness to forgive.
In his relationship with his mentors, it might change the dynamic of how they guide him. Instead of using physical gestures like a hand on the shoulder for reassurance, they would have to rely more on verbal communication. This could make the bond-building process more challenging as physical touch is often a way to convey closeness and trust in these relationships.
Maybe he has some personal grudges or misunderstandings within the family in the fanfiction. It could be that something happened in the past that made him feel betrayed or unappreciated, so he refuses to offer help.
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.