Naruto might be shocked at first. He has always seen Sakura as a friend, so being beaten up by her would be unexpected. He could try to talk to her and figure out what's wrong.
Sasuke could be one. Given their complex relationship, there could be a situation where Sasuke's newfound power or different ideology leads him to fight and beat Naruto in a fan - made story.
In some fanfictions, Naruto might get beat up when facing a powerful new villain who has some unknown jutsu. This could be a villain created by the fanfic writer to test Naruto's limits.
One possibility is that there's a misunderstanding between Naruto and Karui. Maybe Karui thinks Naruto has something to do with Sasuke's actions that have affected her village. So, in her anger, she attacks Naruto.
Well, in a lot of these fanfictions, Stiles can get beat up due to his own recklessness. He might be so determined to solve a mystery or help his friends that he doesn't think about the consequences and ends up in a dangerous situation where he is outnumbered and beaten up. Also, there could be miscommunication. Maybe someone thinks he has done something wrong when he actually hasn't, and they take matters into their own hands and beat him up.
Well, it might be that the fanfiction focuses too much on Sakura in a way that Naruto feels is unfair to the other characters. Naruto is part of a big world with many important people, and if the fanfic just hones in on Sakura all the time, he could get fed up. Also, if the fanfiction has Sakura constantly putting Naruto down or not appreciating his efforts like in the real story, that could be a reason.
Maybe some new kids in the neighborhood who are trying to establish their dominance and pick on Lincoln as an easy target. They might not know much about him or his family, but just see him as someone they can bully.
It could be an antagonist character in the Septiplier fanfiction world. Maybe someone who has a grudge against Jack for some reason, like a rival in a game or a love interest situation gone sour.
It could lead to a shift in the type of fanfictions being produced. If Naruto getting fed up with Sakura fanfiction becomes a popular concept, more fanfic writers might avoid writing in that vein or might try to rewrite the relationship in a more acceptable way, which in turn changes the overall landscape of Naruto fanfictions in the fandom.
In some fanfiction scenarios, Sakura could be under the influence of a dark power or a curse. This power might be corrupting her mind and making her lash out at Naruto for no real reason. It could also be a case where Sakura is trying to prove herself as a strong kunoichi and Naruto is just in the wrong place at the wrong time, so she uses him as a target to show off her skills.