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.
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.
It could be a misunderstanding. Perhaps Naruto was involved in an incident where his actions were misinterpreted by his brother. For example, Naruto might have accidentally caused harm to someone his brother cared about while trying to do something good, and his brother didn't get the full story and started to hate him as a result.
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.
Another reason might be related to family politics. In some complex family structures in the Naruto universe, there could be different factions. Naruto might be on the wrong side of the power struggle within the family. His views or actions could be seen as a threat to the traditional power structure of the family, so they hate him.
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.
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.
It could also be that Naruto has been influenced by some external force in the fanfiction. For instance, an enemy might have planted false memories or ideas in his head, making him believe that his parents and sister are bad. This false perception could then fuel his hatred.