Perhaps Naruto blames Kakashi for not being able to prevent some bad things from happening. For example, if a friend of Naruto gets hurt during a mission that Kakashi led, Naruto could hold it against him. Kakashi, as the leader, might seem responsible in Naruto's eyes.
It could also be that Naruto has different ideals from Kakashi. Naruto is very straightforward and eager to prove himself, while Kakashi has his own more reserved and complex way of doing things. This difference in approach might lead to Naruto feeling that Kakashi doesn't understand him and thus hating him.
One possible reason could be that Naruto might feel Kakashi is too strict with his training. Maybe Kakashi's methods are too harsh for Naruto, making him frustrated and gradually developing dislike.
One possible reason could be that in the fanfiction, Kakashi might have made a decision during a mission that Naruto strongly disagreed with. For example, Kakashi could have chosen to sacrifice something important to Naruto in order to achieve the overall mission objective.
One reason might be that he doesn't like how fanfiction can change the relationships between characters. For example, in the original, his relationship with Naruto is based on training and mentorship, but fanfiction could make it something completely different.
It could also be due to a misunderstanding. Kakashi might be keeping some secrets from Naruto, like information about his parents or some hidden power within him. Naruto, being curious and eager for answers, could misinterpret Kakashi's motives for secrecy as a sign of distrust or dislike, which then turns into hatred.
Perhaps he thinks fanfic undermines the integrity of the original Naruto story. The official story has a certain narrative and character development, and fanfic can deviate from that significantly. When it comes to his connection with Naruto, any deviation in fanfic might be seen as a negative. For example, if a fanfic changes the way he mentors Naruto, it could be something he wouldn't like.
Perhaps in this fanfiction's universe, Naruto's goals and ideals are completely different from Kakashi and Sakura's. Naruto may be aiming for a more radical change in the ninja world, while Kakashi and Sakura are more conservative. Their differences could lead to Naruto developing a sense of hatred towards them as they constantly oppose his ideas.
One possible reason could be that Kakashi is preoccupied with other important matters in the village. Maybe he has some top - secret missions or tasks assigned by the Hokage that demand his full attention, leaving him with little time to focus on Naruto.
One possible reason could be Kakashi's reputation as a strict and powerful teacher. Naruto might be in awe of his skills and fear making mistakes in front of him.
One possible reason could be that Naruto might be trying to prove his independence. He has grown and wants to show that he can handle things on his own without always relying on Kakashi's guidance.
Perhaps there was some sort of dark influence or mind - control at play. An enemy might have manipulated Kakashi's mind in such a way that he believed Naruto was a threat and thus left him for dead, not realizing his true self.
Another reason could be that in this fanfiction, the plot is set in a way that there is a new training system in the village. And this system doesn't involve Kakashi in Naruto's training. There could be new mentors or a completely different approach to training young ninjas like Naruto, which excludes Kakashi from the equation.