Well, in certain fanfic concepts, Naruto's character might be twisted a bit. The author could be exploring a 'what - if' scenario where Naruto has a falling - out with the Rookie Nine. It might start from a small incident, like a failed mission where the blame is wrongly placed on Naruto. Over time, this could fester and turn into hatred as Naruto feels betrayed by his so - called friends in the Rookie Nine.
It could be that in the fanfic's storyline, the Rookie Nine have made some choices that go against Naruto's ideals. For example, if they side with a character or a group that Naruto sees as wrong. This could lead to his hatred. Also, perhaps there has been some miscommunication among them, and Naruto takes it the wrong way, which gradually builds up his negative feelings towards them.