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 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.
Maybe they were jealous of Bell's success or popularity in the story.
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.
Perhaps they misunderstand Sakura's relationship with Naruto. They might think she has romantic feelings for him when Naruto's parents have other plans for their son, so they yell at her to keep her away.
Another reason could be that Naruto is lured away by an external force. Some powerful figure or group might convince him that leaving his parents is for the greater good, perhaps in the name of protecting them or the village in a more effective way.
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.
It could also be related to some hidden family secrets or prophecies. Maybe there was a prophecy that Naruto would bring great destruction in the future and Kushina, believing in it, thought she had to stop him before it was too late. This would be a very complex and heart - wrenching betrayal if it was based on such a false premonition.
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.
He might be mind - controlled. Some dark magic or an evil character could take over Naruto's mind and force him to act against the ponies in the MLP world.