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.
The fanfiction could develop this hatred through the introduction of new characters. These characters might feed Naruto false information about Minato and Kushina, making him question their motives and ultimately hate them. For example, a character who has a grudge against the Uzumaki family could manipulate Naruto.
One scenario could be that Naruto discovers some hidden secrets about Minato and Kushina that he interprets as them being selfish. For instance, he might find out that they had a choice to be with him but chose something else instead, which makes him angry and full of hatred towards them.
This fanfiction could also change the relationships with other characters. For example, if Kushina hates Minato, the Third Hokage might have to step in more often to mediate between them. And the other villagers might also take sides, creating a divided village atmosphere that is quite different from the united one in the original story.
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 in fanfiction for Naruto hating Minato could be the lack of a normal family life. Naruto was alone most of his life, not knowing his father. If he were to find out about Minato's actions in a negative light, like seeing the sealing as a selfish act to save the village at his expense, he could develop hatred. Fanfictions often take these complex emotions and build stories around them.
Well, in the original story, Naruto idolizes his parents. But in this fanfiction, the hatred is a complete deviation. It changes Naruto's character motivation entirely. Instead of being driven by a desire to live up to his parents' legacies, he's now driven by this negative emotion towards them.
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.
The original Naruto story is built on themes of love, sacrifice, and the pursuit of dreams. When you have a fanfiction where Minato and Kushina hate Naruto, it undermines these themes. For example, Minato's sacrifice in the original was for Naruto's future. But in this fanfiction, that meaning is lost as they are now against Naruto. It's a huge deviation from the positive and motivational elements of the original story.
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.