The mutants were not some idealistic victims of society.

Very much this.

The comics have dealt with a very large range of powers even when it's just been one off characters.

This has included beings so beyond powerful the only way to deal with them was to erased them from ever existing like Matthew Malloy from Uncanny X-Men (3) #23: https://marvel.fandom.com/wiki/Matthew_Malloy_(Earth-14923).

Originally his powers manifest in full after being confronted by existing PTSD of his wife dying in front of him during an alien attack years earlier. When he meets his wife's sister she tries to talk to him about the past and he snaps. With so much existing suppression he quite literally explodes and nukes the town he lives in.

On a more tragic note was a teenager in Ultimate X-Men 41 that manifested the power to secrete toxins that burned organic material within a radius. This included his family before he woke up, people he walked past on his way to school, everyone at his school once there, and his girlfriend right before his eyes.

In the end Wolverine is sent to deal with him to prevent the obvious fallout such an event would cause. Despite Wolverine's bloody history and track record as a killer and assassin through the years he still tries to offer the kid some comfort before the inevitable as nobody else would survive long enough once they got near.

Both tragic characters who have the potential to cause unbelievable levels of death and destruction that for the most part are a consequence of simply existing. There's no malice behind what they do, especially in the teenager's case, they simply are. That's why many are terrified of them, it's tangible dangers that can and have wiped out countless populations through either intentional acts or accidental ones.