It could also be related to her relationship with Sasuke. She might have realized that she used Naruto's feelings for her while she was still hung up on Sasuke, and this unfair treatment of Naruto made her want to say sorry.
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.
Perhaps she made a mistake during a mission that put Naruto in danger. Like she misjudged an enemy's move and Naruto had to bear the brunt of it to save her. This would surely make her feel guilty and lead to an apology.
One reason could be that she realizes she has been too dismissive of Naruto's feelings for her. She might have led him on or been cruel in rejecting his advances in the past. Another reason is that she finally understands how much Naruto has sacrificed for the village and for her personally, and she feels guilty for not showing him more respect and gratitude earlier.
Naruto might be very forgiving right away. He has always had a big heart and cared deeply for Sakura, so he could just accept the apology with a big grin and say it's all in the past.
One reason could be that Naruto is focused on his own goals like becoming Hokage and he might see Sakura's feelings or her actions as distractions. He has a lot on his plate and may not have the time or energy to deal with her in a warm way.
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.
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.
One reason could be Naruto's recklessness. In fanfiction, Naruto might do something extremely dangerous without thinking, and Sakura, being worried about his safety, yells at him. For example, if he decides to take on a powerful enemy alone without a proper plan.
Maybe Naruto is sick of Sakura in fanfiction because her character is often portrayed as too pushy or one - dimensional. In some fanfictions, Sakura might be overly obsessed with Sasuke and Naruto just gets tired of her constantly going on about it.
One reason could be miscommunication. Maybe Sakura said something that Naruto misinterpreted as an insult to his dreams or abilities. For example, if she made a comment about his progress as a ninja in a way that came off as dismissive.
One possible reason could be that Naruto has his own unrequited love for someone else and he is trying to distance himself from Sakura to avoid leading her on. For example, if he has deep feelings for Hinata, he might be cold towards Sakura to make his own feelings clear.