One possible reason could be the pressure associated with the Hokage title. Naruto has always been in the spotlight and being Hokage comes with a huge burden of responsibility. Maybe in the fanfiction, he resents how it restricts his freedom to just be himself and have adventures like he used to.
It could also be that Naruto in the fanfiction has a different view of leadership. He might think that the Hokage role is too traditional and not adaptable enough to modern threats. He may believe that a different form of leadership would be better for the village and his hatred stems from his frustration with the existing Hokage - centered system.
Perhaps he hates the Hokage system in the fanfiction because he sees the corruption or inefficiency within it. He might have witnessed some unfair decisions made by the Hokage or the system that led to the suffering of his friends or the village in general.