One reason could be jealousy. If Sakura shows too much interest in another character, Naruto might feel jealous and punish her in a childish way, like ignoring her for a while.
It could be due to her overconfidence. If Sakura's overconfidence leads to a bad situation for the group, Naruto, who values the safety and unity of the team, might punish her. He may make her do extra chores or training to teach her a lesson about humility.
If Sakura breaks a promise to Naruto, especially one related to their ninja code or their personal bond, Naruto may feel the need to punish her. This could be in the form of not sharing important information with her or making her face the consequences of her broken promise on her own for a while, so she understands the importance of keeping her word.
She might be jealous. Maybe Naruto has achieved something that Sakura has been striving for, like getting recognition from a certain person or mastering a new jutsu. Her jealousy could get the better of her and lead to her lashing out and injuring Naruto.
Well, in some fanfictions, Dumbledore might want to punish Hermione if she goes against the school rules in a way that he thinks is particularly serious. For example, if she delves too deep into dangerous magic without proper authorization.
One reason could be for the sake of the Naruhina relationship. To make Hinata seem like a better match for Naruto, the writer might make Naruto hate Sakura. For example, if Sakura is written as being too pushy or bossy in the fanfiction, Naruto could start to dislike her.
In some fanfictions, Naruto might be influenced by an external force. Maybe a villain has the ability to manipulate emotions, and they target Naruto, making him lose control and hit Sakura back. This then sets up a story arc where Naruto has to overcome this external influence and make amends with Sakura.
It could be that in the fanfiction, Naruto's character is developed in a way that Sakura, within the sasunaru concept, doesn't approve. For instance, if the fanfiction makes Naruto too weak or too different from his original self. Also, if the fanfiction focuses too much on certain relationships that she doesn't like, she would hate it.
One possible reason could be for the sake of creating a more complex love triangle in fanfiction. Maybe the writer wants to explore a different dynamic where Naruto and Hinata's relationship is strengthened by having a common dislike for Sakura. It could also be that the fanfiction writer is trying to give Hinata more agency and make her a stronger character by having her oppose Sakura in some way, perhaps in matters related to Naruto's affections.
In some fanfiction, it could be related to a misinterpretation of character relationships. Maybe the author has a skewed view of Naruto and Sakura's dynamic and decides to create a tragic and unexpected turn of events where Naruto kills Sakura to show the breakdown of their bond.
Well, Naruto has a very warm and persistent personality. He's always there for his friends, and he has a big heart. In fanfiction, Sakura might see these qualities in Naruto and realize his true value. He's the kind of person who can make her laugh and feel safe, which could be very appealing compared to Sasuke's more brooding nature.
One possible reason could be that in some fanfiction, Naruto might be written to hate them because of their early treatment of him. Sakura was often dismissive of Naruto in the beginning, and Ino was more focused on Sasuke too. So in a different narrative, Naruto could hold grudges against them for not seeing his worth initially.
In most cases, it might seem unethical because Naruto and Hinata have a deep bond. If he punishes her without proper investigation or out of anger, it's wrong. But if it's a plot device to show growth and forgiveness in both characters, then it can be an interesting ethical exploration in the fanfiction.