A prevalent theme is the struggle for acceptance. Naruto constantly has to fight against the hatred of the village to be accepted. There can also be themes related to power. For instance, how Naruto uses his power either to prove the village wrong or to protect himself from their hatred. Additionally, themes of friendship in the face of adversity often come up. Despite the village hating him, he may find true friends who stand by him.
One common theme could be Naruto feeling betrayed by Konoha. Maybe he discovers some dark secrets about the village that make him turn against it. For example, if he found out that the village was using shinobi unfairly or was involved in immoral activities.
In some cases, it could be because the writer wants to deviate from the typical 'hero is loved' trope. They might think that exploring a scenario where Naruto is hated in his own village can bring out new aspects of his character. It could also be related to exploring the politics within the village. For example, perhaps there are factions in Konoha that see Naruto as a threat, either because of the Nine - Tails inside him or because they fear his growing power. This kind of fanfiction can dig deep into these political undercurrents.
Some fanfictions have Naruto uncovering dark secrets about Konoha. These secrets could be about the actions of the previous Hokages or the village elders. Discovering these secrets makes Naruto lose faith in Konoha and start to hate it.
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 false accusations. If Naruto is wrongly accused of a major crime in the village and no one believes him, he might start to hate Konoha.
In some fanfics, Naruto might be depicted as hating Konoha. This could be due to various reasons like feeling betrayed by the village's hidden agendas or being mistreated in some alternate storylines.
Another aspect could be related to past traumas. Naruto has been through a lot, and if the Konoha 11, even unintentionally, reminded him of some of the negative experiences he had in Konoha, like the ostracism he faced as a child, it could make him hate them in the fanfiction.
In some fanfictions, Naruto might be depicted as hating Konoha due to feeling betrayed. For example, if the village turns against him unjustly or fails to support him when he needs it most. Maybe they suspect him of something he didn't do, like being involved in a crime against the village, which could lead to his hatred.
One common theme could be betrayal. Naruto's act of not being loyal to Konoha can be seen as a form of betrayal in the context of the original story. Another theme might be self - discovery. As he breaks away from his loyalty to Konoha, he may start to discover new aspects of himself.
A prevalent theme is also the empowerment of the underprivileged. Since Naruto came from a difficult background, he would use his position to ensure that those who were previously overlooked or mistreated have a better chance in Konoha. And there's often the theme of a more peaceful Konoha, where his rules help prevent internal strife and external threats more effectively.