Uhm, actually, yes, it happens.
Not lynched, necessarily; more like, killed by your parents, or killed by your staff, or shot by the cops, or bullied so much that you eventually kill yourself--but, yes, people are killed because they're autistic.
Yeah, it's a different thing from getting lynched because you're gay. Usually murders of GLBT people are done out of active hatred and desire to harm someone. The perpetrators see the gay person as an enemy. In the case of autistic murder victims, the perpetrators usually see the autistic person as non-human, unimportant, or an obstacle to be got rid of. Oh, and they're also more likely to get away scot-free because it's "so stressful" to raise an autistic kid. Well, if they're white, they do. If they're black, they go to jail, because black people don't have access to slick lawyers...er, I mean, black people are violent. Yeah.
See sig for examples.