Perhaps Makarov has done something that Naruto sees as a threat to his village or his friends. Naruto is very protective, so any actions from Makarov that seem harmful could lead to hatred. In the fanfiction world, their personalities might just not mesh well, leading to this negative relationship.
Well, maybe in this fanfiction Naruto has some clashing values with Makarov. Naruto values loyalty and friendship highly, if Makarov somehow goes against these concepts in the fanfic, Naruto could hate him.
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.
One reason could be a misinterpretation of their complex relationship. In the original story, Naruto actually cares deeply for Sasuke. But in fanfiction, the author might be exploring a 'what if' scenario where Naruto's frustration turns to hate due to Sasuke's repeated betrayals. Another reason could be to create a more angsty or dramatic plot. By having Naruto hate Sasuke, it can introduce new conflicts and character developments that are different from the canon.
It could be that the fanfiction creates a forced or contrived situation. Naruto is a character known for his determination and positive energy. A plot where he hates his sister might not fit well with the overall Naruto universe. It might be a way for the author to create drama in a rather unappealing way that doesn't resonate with the essence of the Naruto character.
Maybe the fanfiction portrays Hinata in a way that doesn't align with her true character. For example, it might make her overly aggressive or weak in a way that doesn't fit the original concept.
One reason could be that it goes against the core themes of Naruto's character development. Naruto was always longing for family and his journey was about finding his place in the world which included his family roots. Fanfiction that has him hating family might seem out of character.
One possible reason could be that the original Naruto story has a very distinct and carefully crafted world and character arcs. Fanfiction might distort these in ways that seem disrespectful to the source material, making Naruto, as a character concept, seem to 'hate' it. For example, some fanfictions may change Naruto's core values or relationships in a way that goes against the essence of the character.
Maybe Naruto feels overshadowed by the Rookie 9 in the fanfiction. In the original series, Naruto has his own journey and development. If the fanfiction misrepresents his relationship with the Rookie 9 in a negative way, like making them seem better than him all the time, he could hate it.
One reason could be that Naruto values respect, especially towards women. Perverts in fanfiction might go against this value of his. He has been shown to be protective of his friends, and seeing improper behavior towards them or others in fanfiction would make him dislike it.
Well, in the 'naruto hates zeus fanfiction', it could be due to cultural differences. Naruto's world has a specific Japanese - inspired culture, while Zeus is from Greek mythology. Naruto might resent Zeus for representing a foreign and perhaps overpowering entity that doesn't fit into his understanding of the world.