I'll agree that the anti-vaxxers make it out to be the equivalent of a chemical lobotomy. A lot of B-horror-movie hyperbole about the mysterious poison that turns babies into zombies.
Not being autistic myself, but having struggled for as long as I can remember with moodiness and PTSD, I can only say that concern is warranted for what is a legitimate mental-health epidemic. I can't begin to imagine how the autistic must suffer. I figure it must be like people with locked-in syndrome, who want to express emotion and speech but can't. Or deaf-mutes who long to hear and speak but become frustrated that they can't. The schizophrenic can't turn off the echoes, while the autistic struggles to make a sound.
I don't think it's because of vaccines, obviously. The guy who made Borat has a brother who is a brain scientist, and he says that there is a link to fetal testosterone causing deformities in key areas of the developing brain responsible for things like speech and emotional connectedness. (He nevertheless says that the vaccine-testosterone link is bogus.) He also says that there's something to be said for the idea of it being "Linux syndrome," where a lot of computer scientists and engineers tend to be autistic and that this is an example of an "extreme male mind." He undoubtedly courts controversy for suggesting there are gender differences that contribute to mathematical ability and emotional empathy (and that a deficit in one may be linked to a strength in another), but it sounds like a reasonable theory to investigate. At least more nuanced than letting kids die of measles because of some idiot charlatan's bogus research and Jenny McCarthy's equally idiotic PR campaign.