One possible reason could be that the clan fears his power. In some fanfictions, Naruto's growing strength and his potential to disrupt the clan's traditional power structure might lead to his exile. They may see him as a threat to their established ways.
Another reason could be a false accusation. Maybe someone in the clan frames Naruto for a serious crime. Since he is already an outcast in the village in some ways, it's easier for the clan to believe the false story and exile him to protect their reputation.
It could also be related to a prophecy. The clan might misinterpret a prophecy that involves Naruto. They think that exiling him is the only way to avoid a disaster that they believe he will bring, not realizing that they are actually making things worse by doing so.
In this fanfiction, Naruto could reject his clan because of the dark secrets or past actions of the clan. He is a character who values justice and friendship. If the clan has a history of wrongdoings that he discovers, he may not want to be associated with it. Also, Naruto has his own dreams and goals that might not fit within the framework of the clan. He has always been a bit of a rebel, and rejecting the clan could be his way of standing up for what he believes in.
One possible reason could be to seek greater power and training opportunities elsewhere. Maybe he feels restricted within his clan in terms of the type of jutsu he can learn or the level of training he can receive. So, he decides to leave to explore different ninja arts and grow stronger on his own terms.
It could be due to a prophecy. The Uzumaki clan might have received a prophecy that Naruto would bring great turmoil or change to the clan, and rather than face the uncertainty, they chose to exile him. Some clans in the Naruto universe are very superstitious about prophecies. Also, Naruto's unruly nature as a child could have been misinterpreted. His pranks and disregard for some of the strict clan traditions might have been seen as disrespectful and a sign that he didn't belong in the Uzumaki clan, leading to his exile.
Perhaps there were some dark secrets in his clan that he discovers. These secrets could be related to past wrongdoings, like how they treated other clans or individuals. If Naruto has a strong sense of justice, learning about these things might make him hate his clan. It could also be that he feels ostracized or different within his clan, like if he has abilities or beliefs that are not accepted by the majority of the clan members.
It could be related to some prophecy or superstition within the clan. They might think Naruto is a bad omen or something that goes against their traditional beliefs, so they decide to disown him.
One possible reason could be that he is wrongly accused of a serious crime against the village. For example, if some important secrets are leaked and the village leaders suspect Naruto without proper investigation, they might exile him to safeguard the village's so - called security.
It could be that his sister has some special abilities or talents that the family or the village values more. For example, if she has a very rare and powerful bloodline limit, everyone's attention would be drawn to her. In a ninja world, power and potential are highly regarded, so Naruto might be overlooked because his sister seems to have more of that 'special something' at first glance.
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.
It could be that there was a prophecy related to his sister that made the family think she was more important. For example, a prophecy that she would be the key to saving the village in the future. And in their short - sighted view, they abandoned Naruto to focus all their resources on her.
One possible reason could be fear. Naruto has the Nine - Tailed Fox sealed within him. His clan might have been afraid that this power could bring destruction upon them, so they chose to abandon him. Another reason could be a misunderstanding. Maybe they thought Naruto was somehow in league with the forces that brought the Nine - Tailed Fox to the village in the first place.