One reason could be that the fanfic writer wants to deviate from the original narrative where Naruto gradually gains acceptance. They might want to put him in a situation where he has to struggle more with being unwanted to make the story more interesting. For instance, they could write a scenario where new characters are introduced and they shun Naruto for some reason.
His past experiences of being an orphan and often being shunned or bullied as a child might resurface in the fanfiction. These memories can make him feel alone even when he is surrounded by people. He might feel that no one truly understands what he has been through.
The writing quality in some Pokemon fanfic could be really poor. There might be bad grammar, inconsistent plotlines, or just a general lack of creativity that makes you dislike it. For example, some fanfics just reuse the same old ideas over and over again without adding anything new or interesting to the Pokemon universe.
One reason could be his status as a jinchuriki. People might be afraid of him because of the Nine - Tails inside him, so he feels unloved. Another reason is that he was an orphan, and without his parents around, he may have felt like he didn't have that family love that others had.
Poison or some sort of harmful jutsu effect. Maybe an enemy uses a special poison or a jutsu that slowly weakens Naruto's body. In the fanfic, this could be a new and unique type of attack that he has not encountered before, and his body is not able to withstand it, resulting in fainting.
One reason could be some sort of special jutsu or power - up. Maybe he got a new form or ability that suppresses pain. For example, it could be related to his Sage Mode or something new entirely.
One reason could be that they were comrades. Losing Superman means losing a strong partner in protecting the world.
Well, sometimes it's just a matter of taste. Some people might not like the way Ron is portrayed in certain fanfics. Maybe they prefer a more heroic or different version of him, and when the fanfic doesn't meet that expectation, it becomes unwanted. Also, the writing style of the author can play a role. If it's too convoluted or not engaging enough, it can make the 'Ron Weasley fanfic' unwanted.
Perhaps in the fanfic, Hinata has fallen in love with someone else. It could be a new character introduced in the fanfic's universe or someone she has come to know better over time, leading her to reject Naruto.
In some fanfics, there could be a misunderstanding. Suppose Kushina did something that Naruto misinterpreted as harmful to him or his friends. This misinterpretation could lead to his hatred. For example, if Kushina was involved in a mission that Naruto thought put the village at risk, but in reality, she had no choice.
One reason could be a major betrayal. For example, if his friends turned on him, it might shatter his idealistic view and push him towards violence. In fanfic, an author might explore this by having a false accusation against Naruto within the village, causing him to lose faith in the people he once trusted.