One possible reason could be feeling betrayed by the village's secrets and politics. Maybe he discovers some dark underbelly of the Leaf Village that makes him lose faith in it.
It completely flips the original story. In the original, Naruto loves the Leaf Village and is willing to sacrifice everything for it. In this fanfiction, his hatred changes the dynamic. It might make his relationships with other characters like Sasuke, who also had issues with the village, more complex.
One possible reason could be the way he was treated as a child. He was ostracized and shunned by many villagers because of the Nine - Tails inside him. This constant rejection and coldness from the people around him might have led to his hatred in the fanfiction.
He might become more cynical. Instead of his usual optimistic self, he starts to view the world with a more jaded eye. His relationships with his friends could also be strained. For example, Sasuke might be more understanding of Naruto's hatred, or they could even be on opposite sides if Sasuke still has loyalty to the village.
His hatred might make his relationships with some villagers who support the civilian council strained. For example, those who are influenced by the council's propaganda might distance themselves from Naruto.
The MC's hatred for the village could cause him to go on solo missions that go against the village's interests. Maybe he'll refuse to follow orders in critical situations or even try to undermine the village's leadership. It's a recipe for lots of drama and intense storylines.
One possible reason in fanfiction for Naruto hating Minato could be the lack of a normal family life. Naruto was alone most of his life, not knowing his father. If he were to find out about Minato's actions in a negative light, like seeing the sealing as a selfish act to save the village at his expense, he could develop hatred. Fanfictions often take these complex emotions and build stories around them.
Maybe it's because of the different power systems. Naruto has chakra and his ninja abilities, and Rias has her devil powers. If in the fanfiction these power systems are not properly integrated or if one overshadows the other in an unappealing way, Naruto could be depicted as hating Rias. Say, if Rias' devil powers are made to seem too overpowering and it goes against Naruto's sense of fairness in combat, it could lead to such a scenario.
It could be that the fanfiction simply doesn't meet Boruto's standards for what the Naruto universe should be like. He has grown up in that world and has his own ideas about how things should be. Fanfiction can be very hit - or - miss in terms of quality and faithfulness to the source material. If it's of poor quality or changes things too much, Boruto might hate it.
A possible theme is rivalry. The fanfiction might portray Hinata as a rival to Naruto in some aspect, causing his hatred. For example, in a political or power - struggle context within the Naruto universe.