Perhaps in the fanfiction, there were some misunderstandings. The Konoha 12 might have accidentally or unknowingly done things that hurt Naruto deeply. Maybe they blamed Naruto for something he didn't do, or they took credit for Naruto's achievements. These actions could pile up and make Naruto feel hatred towards them.
One possible reason could be that Naruto might feel overshadowed by the Konoha 12. They all have their own unique skills and family backgrounds. For example, Sasuke is always seen as a prodigy. Naruto, who grew up lonely, could feel a sense of envy or resentment towards them which might be explored in the fanfiction. Also, the Konoha 12 might have some unspoken rules or a clique - like environment that Naruto doesn't fit into, making him develop negative feelings in the context of the fanfiction.
One possible reason could be that Konoha has a history of dark secrets. Maybe Naruto and Kushina discovered some unethical practices within the village that made them lose faith in it. For example, the way the village treated the Uchiha clan was quite unjust. Kushina might have known about some of these underhanded dealings and passed on her concerns to Naruto.
Another reason could be that he witnesses corruption or unfairness within the village leadership. If he sees that the system is rigged against certain groups, including himself or his friends, he could grow to hate Konoha and decide to leave.
One reason could be that Naruto has seen too much death and destruction in Konoha. His 'godlike' state might make him think that the only way to end all the suffering is to destroy the root cause, which is Konoha. He may believe that Konoha's system is so broken that it can't be fixed and needs to be completely eradicated.
The story would deviate from the original themes of unity and friendship. Naruto's hatred could split Konoha into factions. This would mean different training regimens, different missions, and different loyalties. For example, Naruto might start his own group of ninjas who share his views, which would completely change the power dynamics in the village.
They could leave because of a prophecy. Some ancient prophecy might state that they need to leave Konoha to fulfill a greater destiny elsewhere. So they trust in this prophecy and leave their home.
Perhaps Naruto discovers some dark secrets about Konoha that go against his values. Like if the village has been involved in unethical practices that he can't overlook. This could be things like using underhanded tactics against other villages, which would make Naruto, with his strong sense of justice, turn against Konoha.
This type of fanfiction can also affect how new fans perceive the Naruto world. If they stumble upon 'konoha hates naruto' fanfiction first, they might get a very different initial impression of the series compared to those who start with the original story. It can be both a source of new interest, as they might be curious to see how such a different take is developed, or a source of confusion if they are not aware that it is a non - canonical exploration.
It might lead to a decrease in the popularity of yaoi fanfiction within the Naruto fandom. If the general idea that Naruto would hate it spreads, some fans might refrain from creating or consuming such fanfiction out of respect for the character. On the other hand, it could also lead to a backlash from fans who think that fanfiction should be a free - for - all creative space regardless of what the character might think.
Well, in some fanfictions, the idea of Naruto hating Kushina might be a very dark and twisted take. Maybe the author wants to explore extreme emotional scenarios. As for Naruto loving in this context, it could be about different kinds of love - like platonic love for his friends or a romantic love for a character. Fanfiction often takes liberties with the original story's relationships.
There could also be political reasons. Some factions within Konoha might have seen Naruto as a tool or a threat to their own political power. His influence and popularity could have disrupted the existing power balance, leading to animosity from those who wanted to maintain the status quo.