Well, it could be that they find out some 'dark secret' about Naruto. Maybe they think he has some sort of uncontrollable power within him that they fear. Or perhaps they are forced to disown him due to political pressure in the village. There could be a group of elders or powerful clans that demand it in order to protect their own interests or maintain the so - called 'balance' in the village.
It could also be due to some external influence. Perhaps an enemy used some kind of mind - control or manipulation on Kushina. They made her think that Naruto was a threat, so she decided to disown him. In the Naruto universe, there are many powerful villains who could potentially do this kind of thing.
It might be due to jealousy. If Minato was getting more attention or praise in the village for his achievements while Kushina felt overlooked, that could create resentment. Say, Minato was constantly being hailed as a hero for his speed and battle tactics, and Kushina, who also had great power, felt like she was in his shadow.
Perhaps in this fanfiction, there is some sort of misinformation. For example, someone has spread false rumors about Naruto being a threat to the village, and Minato and Kushina believe it without proper investigation. This could lead to their hatred.
One possible reason could be a misunderstanding. Maybe Naruto gets involved in some dangerous situation and they disagree on how to handle it. For example, if Naruto wants to take on a powerful enemy alone but Minato and Kushina think it's too risky.
One possible reason could be a misunderstanding. Maybe some false information was spread about his parents that made Naruto believe they were bad. For example, if there were rumors that Minato sacrificed the village for some other purpose rather than to save it, Naruto might be angry at him.
Well, it could be related to Minato's absences. He was often away on important ninja business. Naruto might have felt abandoned by his father, and Kushina, seeing her son suffer in Minato's absence, could start to resent Minato. Also, there might have been some political decisions Minato made that didn't sit well with Kushina. For example, if he made an alliance that she thought was against the values of the village or their family.
On a more personal level, they could face internal guilt. As Naruto grows up and achieves great things on his own despite their neglect, Minato and Kushina may realize what they've missed out on. This realization could cause them a great deal of internal turmoil and regret for not being there for their son when he needed them.
Perhaps it has to do with a prophecy. They might think that Naruto has a special destiny and that their leaving is a necessary step to set that destiny in motion. They could believe that Naruto needs to grow up on his own to become strong enough to face future challenges.
One possible reason could be for Naruto's protection. Maybe Minato knew of some great danger that was coming for Naruto and he thought that banishing him would keep him out of harm's way. Another reason might be related to some prophecy or hidden power within Naruto that Minato feared could be misused if Naruto stayed in the village.
Perhaps there was a curse or a disease that he couldn't overcome. In some fanfictions, they like to introduce unique and deadly diseases that not even the best medical ninja can cure. It could also be due to a failed mission where he was caught in a trap that was impossible to escape from, leading to his death.