One possible reason could be that Naruto has some sort of power within him that they fear. Maybe it's a power that they don't understand and think could be dangerous, so they hate him out of fear.
In this fanfiction, it could be that Naruto's parents were under some sort of mind - control. Some evil entity could have taken over their minds and made them feel hatred towards Naruto. Also, it might be related to a family secret or feud. There could be something in the family's past that made them believe Naruto was a stain on their family name, even though Naruto himself was innocent. It could also be a case of false information being spread around the village which made his parents believe lies about him.
One possible reason could be a curse. Maybe some enemy put a curse on Naruto's parents that made them forget about him. It could be a way to get back at them by targeting their most precious thing, which is their son.
Maybe they were under some kind of curse or dark magic that made them fear they would harm Naruto if they were close to him.
One possible reason could be that in the fanfic, the author might twist the story to make it seem like his parents' actions had unforeseen consequences that affected Harry negatively. For example, their fight against Voldemort led to Harry being an orphan and having to bear a great burden from a young age.
In these fanfics, a common theme is growth. Harry has to grow up faster and become more independent because of his parents' hatred. Another theme is the search for identity. Without the positive influence of his parents, he has to define himself. And the theme of resilience is also prominent. Harry has to be strong in the face of his parents' negative feelings and all the difficulties that come with it. He has to keep going and not let their hatred break him.
Another reason could be that they had some sort of premonition or prophecy that indicated the Dursleys' place was a crucial part of Harry's future protection. Maybe a seer told them that for Harry to grow into the wizard he needs to be, he has to endure the Dursley experience first.
Yes, there might be. Some fanfics like to subvert the expected negative situation. In these fanfics, even though the start is that Harry's parents hate him, through a series of events such as Harry showing extraordinary courage or kindness, his parents could have a change of heart. For example, he might save them from a great danger, which makes them realize their mistake and start to love him. This kind of plot twist can add more depth and surprise to the fanfic.
It could be that they were misled. For example, they might have been tricked into believing that Naruto was a threat to the village in the future. So, in an attempt to safeguard the village they love, they decided to 'betray' Naruto. This would add a lot of complexity to the story as Naruto discovers the truth later.
In some fanfics, they might abandon Harry because they are under a dark spell. This spell could make them lose their love for him and force them to leave. Another reason could be that they are blackmailed by some powerful dark forces. These forces may threaten their lives if they don't abandon Harry.
One possible reason could be that they are too involved in their own shinobi duties. The world of ninjas is full of dangerous missions, and they might be constantly away on important tasks, leaving Naruto feeling neglected.