Perhaps in the fanfiction, Sakura hurt Naruto's feelings regarding his relationship with Sasuke. Naruto has a deep bond with Sasuke, and if Sakura did something to interfere negatively in their relationship, like trying to force Naruto to give up on Sasuke or saying hurtful things about their friendship, Naruto would likely not forgive her.
It could also be due to Sakura constantly doubting Naruto's abilities in the story. Naruto has always been looked down upon by many in the original series, and if in the fanfiction Sakura continuously expresses her lack of faith in him, it could lead to his unforgiveness. For example, she might have refused to believe in Naruto's new jutsu or his plans to save the village, which made Naruto feel really disappointed and unable to forgive her.