Differences in ideology can also play a part. Tony might have some views on how to handle threats or use technology that the other Avengers don't agree with. Maybe he's more willing to take risks with untested tech that could endanger the team or civilians, which would lead to resentment.
There could be personal grudges from past events. Perhaps Tony made a decision during a mission that had negative consequences for one or more of the Avengers. Like in a fic where he chose to sacrifice a certain area to save a larger population, but that area was important to one of the other heroes.
He might dislike it because it can create false expectations. Fans read fanfiction and might start expecting the real Avengers to act in a certain way that is not in line with their true nature.
He could also become more defiant. Instead of trying to win back their favor, he might double - down on his actions and beliefs. For instance, if they hate him for his use of a particular technology, he might continue to develop it just to prove them wrong.
In fanfic, sometimes the writers want to create drama. By making the Avengers assholes to Tony, they can build up conflict. It could also be related to past events that the fanfic author has created. Maybe Tony made a mistake in the past that the other Avengers can't forgive, even though it was an accident or done with good intentions, and they keep treating him badly.
In some fanfictions, Peter could have a secret that he's keeping from the Avengers. When it's eventually revealed, they might feel betrayed and turn against him. It could be something related to his powers, or his past associations that the Avengers find unacceptable, thus resulting in their hatred.
Maybe he thinks it distorts the real story of the Avengers. Fanfiction often takes the original story and characters in unexpected directions, which might not sit well with him.
One reason could be to explore the extreme consequences of their ideological differences. In the official story, they had disputes over things like the Sokovia Accords. In fanfiction, this could be pushed to the limit, leading to Tony taking Steve's life.
Maybe it's because of some past misunderstandings or conflicts that haven't been resolved.
Blame - placing is also a theme. After disasters or conflicts within the Avengers, Tony is sometimes made the scapegoat in fanfictions. The other Avengers might blame him for the team's problems, whether it's the destruction caused by his inventions or the rifts in the team's relationships. So the fanfictions show the Avengers hating Tony because they hold him responsible for these negative outcomes.
Maybe he thinks fanfiction distorts the real image of the Avengers. He's a proud and complex character who might not like how some fanfiction writers portray him or his team.
One possible reason is that Peter's quick rise to popularity among the public might make the Avengers jealous. They've been around for a long time, and suddenly this young kid is getting all the attention.