It might be due to some kind of memory - wiping jutsu gone wrong. A powerful ninja could have been trying to protect Naruto from something by erasing his parents' memories of him, but it ended up being a total forgetfulness instead of a selective one.
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.
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 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.
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.
Perhaps Naruto has always felt different from others in the village. And when he finally learns about his parents, he realizes that their actions, even if they were for a good cause like protecting the village, still made his life very difficult. He might be angry that they didn't find a better way to handle things so that he didn't have to suffer so much growing up.
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.
It could also be due to a prophecy. Suppose there's a prophecy that Naruto will bring great disaster in the future. His parents, believing in the prophecy, might decide to disown him in an attempt to avoid that future. They might think that by cutting ties with him, they can somehow change the course of events.
It could be that in this fanfiction, there are some external influences like an enemy who has manipulated Naruto's mind. The enemy might have planted false memories or ideas in Naruto's head, making him believe that his parents are not who he thought they were, leading to his rejection.
Well, it could be that Naruto's parents, Minato and Kushina, somehow lose their memories of him. Maybe due to a powerful jutsu gone wrong. Naruto then has to deal with the pain of seeing his parents act as if he doesn't exist. He might try to find a way to reverse the effect, all while still facing the usual challenges in the ninja world.
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.
Another possibility is that they were deceived. There could be a villain who tricked them into believing that giving away Naruto's birthright was the right thing to do. They might have been misinformed about the consequences and the true nature of what they were giving up.