It might be due to a cultural or traditional misunderstanding. In some fan - created cultures within the fanfiction, there could be a certain act that Sakura does which is considered a great insult in Naruto's eyes. Without fully understanding the implications, Naruto punches her in response. For instance, if there's a custom about respecting the Hokage's symbol and Sakura accidentally desecrates it in Naruto's presence while he's in a very patriotic mood.
A reason could be that Sakura says something really hurtful to Naruto about his dreams or his abilities. Naruto, who has always been sensitive about those things deep down, might lose his temper and punch her.
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.
She might leave to find herself. In Konoha, she has always been defined by her relationships with Naruto and Sasuke. Leaving gives her the chance to figure out who she is on her own terms, away from the expectations of her friends and the village.
He might be mind - controlled. Some dark magic or an evil character could take over Naruto's mind and force him to act against the ponies in the MLP world.
I'm not sure if there's a super - popular 'Naruto punch Sakura' fanfic specifically. There are so many Naruto fanfics out there that it's hard to single out one with this exact scenario as being the most popular. However, in the vast expanse of fan - created Naruto stories, it's possible that there are some that feature this plot point.
One possible reason could be that she might have underestimated Naruto in the past. She often belittled his abilities and dreams, but as she grew and realized his true strength and determination, she felt the need to apologize for her previous behavior.
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.
Some authors may write it to add a new dimension to the Naruto universe. Naruto has a huge fan base, and by exploring such a taboo topic, they can attract readers who are interested in seeing a different side of the character. It could also be a form of creative exploration, to see how the story and other characters would react if Naruto were to reach such a low point in his life.
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.
Perhaps Sakura is in a state of extreme stress. Maybe she has a lot of pressure on her, like trying to save a village or a loved one, and Naruto's actions, which might seem reckless to her at the time, cause her to snap and hurt him without really meaning to.
One possible reason could be Sakura's constant pining for Sasuke. Naruto might feel frustrated that she's so focused on Sasuke when he's right there for her. In the Naruto universe, Naruto has always been a bit jealous of Sakura's love for Sasuke, and in fanfiction, this could be amplified to the point where he yells at her out of pent - up emotions.