It could be the village council. They often make decisions for the safety of the village, and if they perceive Naruto as a threat, they might be the ones to lock him away.
One reason could be that some in the village feared his potential as the Jinchuriki of the Nine - Tails. They might have thought locking him away would prevent him from causing chaos. Another reason could be related to those who still held grudges against the Fourth Hokage for sealing the Nine - Tails in Naruto. They took it out on Naruto by imprisoning him.
In this fanfiction, it's possible that Naruto is locked away as a result of a misunderstanding. His powers might be seen as uncontrollable by some in the village. They fear what he could do accidentally with his strength, so they lock him away in an attempt to keep the village safe. However, Naruto being Naruto, he would surely find a way to prove his innocence or break free in the end.
It would make him more resentful. Naruto is a character full of energy and a desire for recognition. Being locked away would deny him the chance to interact with others and gain that recognition. So, he would be angrier at the world that has isolated him.
It could be Danzo. He was always power - hungry and had his own ideas about how the village should be run. He might see Naruto as a threat to his plans, so he locks Naruto away as a baby. He wants to control the village without the interference of the jinchuriki's power.
Well, in this fanfiction, it could be that Naruto is locked away by a powerful enemy of the village who wants to use him as a weapon later. Maybe Orochimaru gets his hands on Naruto as a baby and locks him in one of his secret labs. There, Naruto endures all kinds of experiments and hardships. But through his natural tenacity, he starts to develop unique abilities that are a combination of his jinchuriki powers and Orochimaru's experiments. Eventually, he escapes and has to decide whether to use his new powers for good or for revenge against the village that failed to protect him.
At first, Naruto might be confused and hurt. He doesn't understand why his father would do such a thing to him. He may feel betrayed since he expects his father to be a source of love and protection, not confinement.
It could also be due to a particularly bad encounter with someone in the village. For instance, if he was bullied severely by some older kids and he felt that there was no one to protect him. He might have thought that running away was his only option to avoid further harm.
One possible reason could be for Naruto's protection. His father might think that by locking him away, he can keep Naruto safe from the many threats in the Naruto world, like powerful enemies who might target Naruto for his special powers.
He could rely on his wits. Naruto is a clever kid. He might figure out how to forage for food, like finding edible plants or fishing in nearby streams. Also, he could use natural shelters like caves to stay safe at night.