It could be that Jiraiya was overly harsh on Naruto in the fanfic in his training methods. He might have pushed Naruto too far physically or mentally, and Naruto, instead of seeing it as a way to grow stronger, could have resented it and turned that resentment into hatred over time.
One possible reason could be that in the fanfic, Jiraiya might have made a decision that Naruto strongly disagreed with, like leaving him alone at a crucial time for a long mission. This could make Naruto feel abandoned and thus start to hate him.
One possible reason could be that in this fanfic's unique plot, Jiraiya might have made a decision that Naruto strongly disagreed with. For example, Jiraiya could have been involved in some political intrigue within the ninja world that Naruto thought was against his ideals of justice and peace.
One possible reason could be a misunderstanding. Maybe Naruto overheard some false information about Jiraiya and Tsunade that made him think they had wronged him or someone he cared about. For example, if he heard they were involved in a plot that led to the death of a fellow villager, it could turn his feelings sour.
Perhaps Naruto blames them for some of the hardships he faced. Maybe he thinks that Jiraiya wasn't around enough when he needed a mentor, and Tsunade didn't do enough to support him in certain situations. This could lead to feelings of resentment and hatred in the context of the fanfiction.
Jiraiya was a serious shinobi with a certain code. Fanfiction might play around with that code too much for his liking. It could make light of things he held in high regard, like his loyalty to the Leaf Village or his training of Naruto. So that's a possible reason for his hatred.
One possible reason could be that Naruto feels he has learned all he can from Jiraiya at that point. Maybe he wants to explore his own path independently and test his skills without Jiraiya's constant guidance.
It could also be due to a misunderstanding. Kakashi might be keeping some secrets from Naruto, like information about his parents or some hidden power within him. Naruto, being curious and eager for answers, could misinterpret Kakashi's motives for secrecy as a sign of distrust or dislike, which then turns into hatred.
Maybe in this fanfic, there has been a misinformation spread about Naruto that makes Kushina believe he has done something unforgivable. For example, if false rumors say that Naruto is involved in something evil, Kushina might start to hate him without knowing the truth.
One possible reason could be that Naruto feels he has learned all he can from Jiraiya at that point. Maybe he has reached a level in his training where he believes he needs new experiences and challenges that Jiraiya can no longer provide.
It could be that Naruto has a different view of leadership than Sarutobi. Naruto might see Sarutobi's leadership as being too passive or too focused on maintaining the status quo. He, with his more energetic and revolutionary ideas, may resent Sarutobi for not being more progressive in making the village a better place for everyone, including himself.
One possible reason could be a misinformation plot. Maybe in the fanfiction, Naruto has been led to believe that Yondaime had some dark secrets or did something bad to his family that he discovers later in the story.