It could also be due to a misunderstanding. Perhaps there is some misinformation spread about Sasuke in the fanfiction, like false rumors that he has a hidden and malevolent plan. Naruto, being someone who values their friendship deeply, would be scared at the thought of Sasuke turning into an enemy because of these untrue stories.
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 reason could be Sasuke's thirst for power. If he believes Naruto is the only obstacle in his path to ultimate power, he might be driven to kill him. In some fanfictions, Sasuke may be influenced by a dark entity that twists his mind into thinking Naruto is a threat that needs to be eliminated.
One possible reason could be jealousy. Maybe in the fanfiction, Naruto feels overshadowed by Sasuke in Sakura's eyes, which leads to his hatred. Another reason might be that he perceives their relationship as a threat to his own bonds with them. For example, he could think that Sasuke and Sakura's closeness excludes him in some way.
Another reason might be related to their different ideologies within the ANBU. Naruto may have believed in a more collaborative and friendly approach within the organization, while Sasuke might have been more focused on individual achievement and power. This fundamental difference could lead to Naruto hating Sasuke in the fanfiction.
One possible reason could be to protect Hinata. Maybe Sasuke has unknowingly made a move or decision that Naruto perceives as a threat to Hinata, so he scares Sasuke to make him back off.
In some fanfictions, Naruto might reject Sasuke because of Sasuke's continuous pursuit of power in a way that endangers others. Naruto, who values friendship and the safety of the village, could see this as a betrayal of their shared values.
Maybe Naruto was trying to protect Sasuke from a certain danger. There could be a curse or a powerful enemy that targets male shinobi. So, Naruto uses a risky jutsu to transform Sasuke into a girl to keep him safe. Or it could be that Naruto found a strange ancient scroll with a transformation technique that he thought was something else and when he used it on Sasuke, it turned him into a girl.
One possible reason could be jealousy. Maybe fem Sasuke is jealous of Naruto's natural charisma or his ability to make friends easily. Another reason might be related to their different goals. If fem Sasuke has a very different view of how to save or change the ninja world compared to Naruto, it could lead to hatred.
One possible reason could be his deep connection with Naruto in the original story. Fanfiction might offer new and different perspectives on their relationship, which intrigues him. Maybe he wants to see how others interpret their bond, whether it's their friendship or the complex rivalry. Another reason could be that fanfiction allows him to exist in scenarios that didn't happen in the official storyline, giving him a chance to explore different aspects of his character and his interactions with other characters.
One reason could be that Sasuke realizes he needs Naruto's unique abilities. Naruto has the Nine - Tails' power which could be useful in a certain task. So he takes Naruto with him to achieve a common goal.