It could be that Naruto's own dreams and goals are so different from Sakura's. Naruto wants to be the Hokage and bring peace to the village in his own way. Sakura's goals are more centered around being a good medical ninja and being with Sasuke. Their different paths in life might make Naruto not interested in her romantically as they don't share the same overarching vision.
One reason could be that Naruto has always been more attracted to those who understand his outcast past better. Sakura doesn't really have that kind of connection with him as she comes from a more normal background. So there's a lack of that fundamental understanding between them which hinders any romantic feelings.
One possible reason could be that Naruto's character development leads him to focus more on other aspects like his ninja duties or his bond with other friends. As he grows, his priorities shift.
One reason could be that the fanfiction changes Kakashi's teaching methods too much. Naruto is used to Kakashi's unique style in the original story, and if it's drastically altered in a way that doesn't seem right to Naruto, he might not like it.
In certain fanfictions, Naruto might have a pre - existing relationship or unrequited love for someone else. This could make him overlook Hinata or even seem to dislike her because his heart is set on another character.
Well, Naruto has always been there for Sasuke in the original story. In fanfiction, Fem Sasuke might secretly like Naruto because she sees his loyalty. He's constantly trying to bring Sasuke back to the right path. This loyalty could translate into a deeper affection in the fan - created stories.
One reason could be jealousy. If in the fanfic, Sakura gets closer to someone else Naruto cares about, like Sasuke in a different way than he expected, it might make him hate her. For example, if Sakura teams up with Sasuke against Naruto's wishes in the fan - created plot.
In some fanfictions, it could be due to unrequited love. If Naruto has deep feelings for Sakura but she continuously rejects him in a cruel or thoughtless way, Naruto might feel angry enough to seek revenge. For example, she could publicly humiliate him for his feelings, which would hurt Naruto deeply and lead to thoughts of revenge. Another reason could be a misunderstanding. Suppose Sakura is misjudged by Naruto as having done something terrible when in fact she was innocent. But Naruto, in his ignorance, decides to take revenge. This can create a lot of drama and conflict in the fanfiction.
In some fanfics, Naruto may ignore Sakura because he has his own emotional traumas to deal with. He might find Sakura's presence a reminder of things he wants to forget or move past, so he chooses to keep his distance. For example, if he has faced a lot of rejection from her in the past, he could decide to just cut her out of his life.
Maybe in the fanfiction, Naruto's positive and energetic personality attracts Ino more. He is always so full of life and has a big heart.
Well, it could be that in this fanfiction, Naruto has some sort of hidden agenda. He might call Sakura ugly as a form of reverse psychology. He could be thinking that by doing so, she'll prove him wrong and become more confident. Or perhaps there's some miscommunication or misunderstanding between them. For example, Naruto misheard someone talking about Sakura in a negative way regarding her looks and he wrongly believes it, so he says she's ugly.
Perhaps there was some sort of dark influence at play. In the world of Naruto, there are often dark forces and genjutsu (illusion techniques). It's possible that Naruto was under the influence of a genjutsu that made him see Sakura as a threat, so he punched her in self - defense without realizing it was an illusion.