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So, what is it about Sonic and Minecraft specifically that cause people to draw this connection?
If you performed a search of this site for just "Sonic" you come up with roughly 10,000 posts that mention it. (A little more but I am subtracting a fair amount for other meanings of the word such as "sonic boom" etc after reviewing ten pages worth of just search results.) I am sure given the overly honest nature of some people on the spectrum that a lot have stated they have autism in other forums throughout the internet and have shared their interest in sonic and minecraft openly and obsessively. Giving way to the stereotype of autistic individuals love sonic/minecraft/mlp/etc. They are also games/activities done in solitary or with minimum social contact. Making them ripe for autistic individuals to be drawn to them.
I personally don't find the interest in either, or any anime, but I don't begrudge the stereotype, because of the proliferation of readily available examples of it. People make generalizations to explain what they are exposed to, without really questioning the basis of the generalization. It's how they make something they don't understand more palpable. Since there are incidences of people with autism discussing these interests, it's generalized that people with autism like those interests. Unfortunately, many people are not capable of understanding more or don't have the willingness to try to understand more, so it goes unquestioned.
It happens with a lot of things and is a general rule of human nature. Like all birds are dumb, because of their small brains, all southerners (in the states) talk slow (I wish they did, a lot of them sound like a machine gun with a stuck trigger to me aka: they talk really fast and don't enunciate), etc. The vast majority of people (even autistic) are not experts in autism so the generalizations work for them to explain and define autism.
I look it at as it could be worse. Could be generalized with liking to smear pooh on the walls (some autistic and non autistic individuals do) or something equally as unpleasant and personally untrue.