In some cases, it might be the result of someone wanting to create an alternate universe that is very different from the original. But when doing so, they should still consider the moral and ethical implications. Writing a plot where Kushina cheats on Minato is not only disrespectful to the original story but also to the fans who love the positive aspects of the Naruto world.
Some people might write such fanfiction out of a desire for shock value. They think that by creating a completely different and controversial story, they can attract more attention. But this is a wrong approach as it distorts the original characters.
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.
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.
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.
It could be that Naruto is trying to prove himself. He wants to show that he can be as great a fighter as his father. Also, he might have received some training or knowledge transfer from someone who knew Minato well. This could have inspired him to adopt Minato's fighting style. He may also be in a situation where his normal fighting style isn't working, so he turns to Minato's as a last resort.
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.
I'm not aware of any Naruto fanfiction with such a distasteful plot. The Naruto series is mainly about friendship, love within family and between comrades, and the pursuit of dreams. This kind of content that violates the positive values of the original work is not something that should be promoted in the fanfiction community.
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.
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.
Another reason could be to give more spotlight to other characters. If Minato and Kushina are bashed or made less important, it allows other characters to step up and have more significant roles. This can add depth to characters that might have been overshadowed by Minato and Kushina in the original story. For example, some side characters could get a chance to shine and have their own character arcs that are not possible when Minato and Kushina are in the center of the story all the time.