It could be due to some kind of trauma. Suppose Naruto witnessed his family causing great harm to others when he was young. This might make him repress any positive feelings towards them. He may see them as villains and thus not feel the normal family affection.
One possible reason could be a different upbringing in the fanfiction's alternate universe. Maybe he was raised in isolation or by people who influenced him to suppress family feelings. For example, if he was raised by a group that emphasized self - reliance above all else, he might grow up thinking family bonds are a weakness.
One possible reason could be some kind of dark magic or curse that has been placed on him. Maybe an enemy wants to weaken him by taking away his emotions so he can't fight with his usual passion.
One possible reason could be a misunderstanding. Maybe there was some miscommunication in the past that led Naruto to believe his family didn't understand him. For example, if his family had different expectations for his future as a ninja compared to his own dreams.
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 reason could be some sort of special jutsu or power - up. Maybe he got a new form or ability that suppresses pain. For example, it could be related to his Sage Mode or something new entirely.
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 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.
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.
Well, perhaps in this fanfiction, Kushina did something that violated Naruto's principles. Naruto has always been about loyalty and hard work. If Kushina did something like betraying the village or his friends, Naruto, being the stubborn and principled person he is, might not forgive her. Also, it could be that Kushina was absent during some crucial moments in Naruto's life and he holds a grudge for that.
One possible reason could be a long - held grudge. Maybe there were past incidents in the family that made Harry feel betrayed or neglected. For example, if his family always favored another sibling over him, it could lead to his apathy.