Well, it could be a combination of things. Maybe he saw through some hidden agendas of the village elders or was constantly overlooked for important missions despite his skills. Maybe there were trust issues with his teammates or mentors that built up over time and caused this hatred.
It could also be due to a lack of support. Naruto was constantly in trouble and trying to prove himself. If his family didn't show up in any way to support him and Konoha didn't do enough to encourage him in a positive way, but rather just punished him for his pranks, he might grow to hate them both.
It completely flips the original story. In the original, Naruto loves Konoha and eventually comes to terms with his family legacy. But in this fanfic, the hatred changes his character motivation. Instead of striving to protect Konoha, he might be out to get revenge or simply distance himself from it.
It could be that in the fanfic, Team 7 starts to act in a way that goes against Naruto's moral code. For example, if they start using cruel or unethical methods to achieve their goals. Naruto, being the character he is, would not stand for such behavior and this could lead to his hatred. Additionally, if there is a personal loss that Naruto experiences which he blames on Team 7, that would also contribute to his negative feelings.
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.
The first consequence could be a breakdown in the village's unity. Naruto is seen as a hero in Konoha, and if he turns against it, many of his supporters might be confused or even follow his lead. This could lead to internal strife within the village.
Naruto would be more rebellious. He's always been about friendship and the will of fire in the original story. But under Danzo's leadership, which is more authoritarian, Naruto would likely oppose many of Danzo's harsh policies. For example, if Danzo tried to limit the rights of the Uzumaki clan members, Naruto would be at the forefront of the resistance. Sakura might be more conflicted. She respects authority, but Danzo's methods would make her question her loyalty. Sasuke would probably see Danzo as a target. Since Sasuke is after revenge against those who wronged his clan, Danzo's often - shady actions would put him in Sasuke's crosshairs.
Perhaps there is an event where Naruto's team blames him for a failed mission, even though it wasn't his fault. This could make him resent them.
One possible reason could be the lack of presence of his parents. Growing up without them, he might feel abandoned. And as for Konoha, if he hates it, it could be due to the way he was treated as an outcast, despite being the son of important figures. Maybe the villagers' coldness towards him made him resent the village that didn't seem to protect him from that.
A potential plot twist could be that Naruto's hatred is actually a cover - up for his love. He might be pretending to hate Konoha and his family to protect them from a greater threat. Maybe there's an enemy who would target them if Naruto showed any affection, so he creates this false front of hatred.
Another way is through his attitude towards the villagers. He would show no respect or kindness to them. Instead, he would be cold and hostile, perhaps even going as far as to physically intimidate those who cross his path in Konoha.