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.
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.
There's a fanfic called 'Minato's Return'. In this story, Minato somehow returns and gets to see Naruto's growth. It's really interesting to see how he interacts with Kushina, who is also there in the story, and how they both guide Naruto in new ways. The descriptions of their family bond are heartwarming.
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.
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.
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.
One great fanfic is 'The Early Days of Naruto' which beautifully depicts Minato and Kushina's relationship with baby Naruto. It shows their tender moments together and how they start to teach Naruto about the ninja world from a very young age. Another good one is 'Naruto's Family Beginnings' where the focus is more on the family dynamic. You can really feel the love Minato and Kushina have for their baby. And then there's 'Baby Naruto's World' which goes into detail about how Naruto's presence affects the village even as a baby, and how Minato and Kushina are at the center of protecting and nurturing him.