One possible reason could be a very different and perhaps unappealing take on Naruto's character in that fanfiction. Maybe the author made him overly cruel or out of character in ways that fans who love the original Naruto can't stand.
It could be that the fanfiction involves a really dark or disturbing plot that somehow involves Naruto in a negative light. For example, if it makes Naruto a villain who commits heinous acts against his friends and the village, fans who are used to his heroic nature would likely hate it. Also, if the writing quality is poor and Naruto is just a means to create a chaotic or senseless story, that would also lead to dislike.
Perhaps the fanfiction completely misinterprets the Naruto universe's themes and values. Naruto is all about friendship, hard work, and never giving up. If the fanfiction goes against these core ideas and portrays Naruto as someone who abandons his friends or gives up easily, it would be hated by fans. Another aspect could be if it changes Naruto's relationships in a way that doesn't make sense, like making him enemies with characters he was originally close to in the anime or manga.
One reason could be his power. His connection to the Nine - Tails makes him extremely powerful. In fanfiction, some in Konoha might fear this power and thus hate him. Another reason could be jealousy. Naruto becomes very popular and respected in the original story. But in fanfiction, some characters might be jealous of his achievements and turn that into hatred.
One possible reason could be a false accusation. Maybe someone spread a rumor that Naruto was involved in a heinous act, and without proper investigation, everyone turned against him.
Another reason might be related to a past event that Naruto unknowingly caused harm to one of the Team 7 members' families. Even if it was an accident, the emotional pain could make the affected member, and maybe the whole team, hold a grudge against Naruto. For instance, if Naruto's actions during a battle led to the destruction of a family's home, and a Team 7 member was from that family.
In some fanfictions, Naruto might be hated by his friends due to a misunderstanding. For example, if there's a false rumor spread about him being a traitor. Another reason could be his sudden increase in power that makes his friends jealous. Maybe he accidentally harms one of them during a training session and they hold a grudge.
In some fanfictions, it could be due to outside influence. For example, an enemy might use some kind of mind - control or false information to make Naruto's friends turn against him. Also, Naruto's own actions that are misinterpreted can lead to this. Say he tries to protect his friends in a way that seems wrong to them at first glance, like using a dangerous jutsu near them to fend off an attack.
It could also be due to a past event that Naruto unknowingly was involved in. Maybe something bad happened to Sarutobi's family or friends and he blames Naruto for it, whether it was Naruto's fault or not. For instance, if there was an attack on the village and Sarutobi lost someone close, and he wrongly believes Naruto had a part to play in it, he would start to hate Naruto.
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.
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 envy. If Naruto suddenly gains a great deal of power or attention in the fanfiction, his friends might feel left out or jealous. Another reason could be a misunderstanding. Maybe Naruto is framed for something he didn't do, and his friends believe the false accusations without giving him a chance to explain. Also, in some fanfiction, a change in Naruto's personality, like becoming overly aggressive or secretive, could lead to his friends growing to dislike him.
Sometimes it could be due to a misunderstanding. A game character might be on a quest that the family doesn't understand. For instance, the character might be trying to prevent a greater evil but has to use methods that seem unethical to the family. Without proper communication, the family could misinterpret the character's actions and come to hate them. Also, if the character is born with a 'curse' or some special ability that the family fears, they may be ostracized and hated by the family.