One possible reason could be that they are too focused on their own problems or duties. Maybe they are involved in some important shinobi business that takes up all their time and attention, causing them to overlook Naruto.
Perhaps there is some sort of family secret or past event that makes them act this way towards Naruto. For example, there could be a prophecy or something related to Naruto that scares them, and instead of dealing with it in a positive way, they choose to neglect him.
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.
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 reason could be that his siblings have some special abilities or talents that overshadow Naruto. In the ninja world, those with unique powers often get more attention. So, if his siblings possess something extraordinary, Naruto might be pushed to the side.
In this kind of fanfic, Naruto might first feel a great deal of sadness. He could start to distance himself from his family. Maybe he focuses more on his training, pouring all his energy into becoming stronger so that he can prove himself without relying on his family's recognition.
One possible reason could be that they are too involved in their own shinobi duties. The world of ninjas is full of dangerous missions, and they might be constantly away on important tasks, leaving Naruto feeling neglected.
Maybe he's been influenced by someone who has a different view of heritage. For example, if he meets a character who believes that one should create their own identity rather than relying on heritage, Naruto could be swayed. Another possibility is that he has some sort of resentment towards his heritage. Perhaps there are things in his family's past or in the traditions associated with his heritage that he doesn't agree with or is ashamed of.
He might focus on his training more. By pouring all his energy into getting stronger, he can distract himself from the pain of family neglect. For example, he could spend long hours practicing new jutsu or improving his physical abilities.
In the fanfic, Kakashi might neglect Naruto's training due to a variety of reasons. He could be preoccupied with his own research or a secret mission that demands his full attention. There could also be a misunderstanding between him and Naruto. Maybe Naruto has done something that Kakashi misinterprets, causing him to distance himself from Naruto's training. Additionally, the fanfic could introduce new characters or plot elements that draw Kakashi's focus away from Naruto. For example, a new threat to the village that Kakashi feels he must handle alone, thus neglecting his duties as Naruto's trainer.
In some fanfics, it could be related to a prophecy. His family might believe that Naruto is going to bring about a great disaster according to a misinterpreted prophecy. So, they turn on him in an attempt to prevent the prophecy from coming true, even though they are wrong in their understanding.