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.
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.
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.
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.
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.
Perhaps in the fanfic, there is a prophecy that says Naruto's friends will be the cause of his downfall. So, Naruto, fearing for his future and the safety of the village, starts to distance himself from them and eventually hates them. Or maybe his friends accidentally cause the death of someone Naruto loves dearly, which makes him unable to forgive them.
It could also be due to differences in values. If Dark Naruto had different beliefs about power, friendship, or loyalty compared to his family, and they constantly clashed over these, it might lead to his hatred. For instance, if his family adhered strictly to Konoha's traditional values but he saw them as restrictive.
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.
One way to justify it could be through a series of betrayals. Maybe Naruto discovers that Konoha has been using him all along, and his family has some dark secrets that make him feel betrayed. For example, if he finds out that his father was involved in some unethical experiments that led to the suffering of many villagers, that could turn him against both Konoha and his family.