One reason could be that she has seen Naruto in some really tough situations and is afraid of losing him. Maybe she witnessed a near - death experience of Naruto's and that triggered her overprotective side. Another possibility is that she has grown to understand Naruto's importance not just to her, but to the whole village. So, she feels it's her duty to safeguard him.
She might have realized how much Naruto has sacrificed for her and their friends. His selfless acts could have made her feel that she needs to protect him in return.
One reason could be guilt. Since Minato wasn't there for Naruto when he was growing up in the original story, in the fanfiction, he might be overcompensating for that lost time. He feels like he has to make up for all those years he wasn't around to protect his son.
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 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.
One possible reason could be that she sacrifices herself to save Naruto from a powerful enemy. In the heat of battle, she might put herself in harm's way to ensure Naruto's survival.
Well, some writers may be trying to create a more 'gritty' or 'realistic' version of the Naruto universe in their eyes. They might think that adding an element of abuse to Sakura's story can add more depth and drama. However, they may not fully consider the negative impact it can have on the character and the fans who love her. Also, it could be a way for the writer to express their own darker emotions or experiences through the fanfiction, although this is not a very healthy or appropriate way in this context.
One possible reason could be that Naruto has a different love interest in his heart, like Hinata. In the original story, his relationship with Sakura was more of a friendship - like bond. Another reason might be for the sake of creating an unexpected plot twist in the fanfiction. Maybe the writer wants to explore different emotional and relationship dynamics that don't follow the typical Naruto - Sakura pairing.
Maybe Naruto realizes that his feelings for Sakura are not as strong as he once thought. In the fanfiction, he could have met someone else or had an epiphany about his own emotions. He might leave Sakura to find his true self and explore different relationships.
One possible reason could be that Sakura realizes she has different goals or values that are not compatible with being around Naruto. Maybe she discovers a new path in life that doesn't involve him, such as focusing on her own medical ninja career without Naruto's chaotic lifestyle interfering.
Maybe he's frustrated with her lack of progress in combat compared to him and Sasuke. He could also be in a bad mood and say it without really meaning it.