My personal theory on why this occurs (I have autism myself, and i don't intend this to be a condemnation): Real-life autism often involves the person with autism having passions (and sometimes obsessions) that are much stronger or otherwise remarkable than the average person. However, autism also comes with handicapped social and/or behavioral skills, so it's more difficult to control their passions and to otherwise act appropriately about it. (I.E: they talk endlessly about their respective interests and absolutely refuse to talk about anything else, giving off the impression that their life revolves around said interest; or throwing a fit whenever their interest is criticized or they otherwise don't get their way). This comes into stark contrast with a neurotypical person who is just as passionate: they've had an easier time learning social skills and behaviors, so they can behave themselves much more appropriately.
However, when the passion in question is belonging to a certain fandom (Say Sonic the Hedgehog, Star Wars, Pokemon, the Furry Fandom, or the Bronies), the lines for some reason become blurred. Take this article on Fan Dumb for example. When people get passionate about whatever franchise, they sometimes tend to exhibit behaviors that are just like people with autism who never learned how to appropriately handle their neuroses. My theory is that, to the average person, they end-up appearing to be the same kind of thing.
People with autism have a very negative reputation on the internet as being incredibly spoiled and childish, since the ones who are the most visible are the ones who never learned how to act appropriately in public. And when you see a 20 year old man throwing a temper tantrum at a McDonalds because his Happy Meal had Berry Punch instead of Pinkie Pie, it's kind of hard to be sympathetic towards that person.
So, "autistic" ends up being used as an insult to be laid at these people, whether they actually do have autism or not. And more often then not, the people insulting them don't even know what "autistic" actually means (someone with a disorder that typically includes a handicapped ability to pick up non-verbal communication), since they're only familiar with the stereotype and are big enough idiots to believe that those stereotypes are true.
If any of that made any sense.