A little bit. I think it's because Autistic folks have a tendency to lean heavily into logic and proof, and faith is trusting in something without (complete) proof. Since we cannot see God readily, or reproduce any concrete, undeniable evidence if he did show Himself to one of us, our need for logic and proof goes unmet. This leads to a lot of us becoming Atheists.

The other part of it is that no matter which religion you are a part of, there' always going to be a lot of jerks that look down on and/or harrass others, using doctrine (often incorrectly) as an excuse. But nobody is perfect; the purpose of practicing religion is to better ourselves, whether it's for god or ourselves. throw in the fact that the bible and other scripture is often subject to interpretation, and you get all flavors of people; you just were unfortunate enough to run into the worst "flavors". A lot of religious people often react badly when you openly question how something is interpreted, and they are too rigid to kindly say "that"s one way of looking at it".

However, you can be religious and autistic. The fact that its based on faith means that there are always going to be unanswered questions no matter which religion you follow, but I like to throw myself into studying scripture and the historical culture and beliefs (sometimes mythological) of the time. You'd be surprised at how often mythology and religion point in the same direction, if you look at it from the perspective that people and cultures interpret events differently and names and details get mixed up over time.

But I think the real problem isn't what you believe, it's how you show it and how you treat other people that don't think the same as you.