I am really sorry your son is going through this, OP.
My son is fine with kids with special needs. I don't know if it's inherent, or the fact his older brother has autism and is very low functioning. He actually treats them equally, which can be both good and bad. If a child with special needs has more behavioral issues (one kid in his 1st grade class with sensory issues liked to hit others), he will get mad at him. And since that kid hit more than others may have, my son was mad at him more often. Same with a kid in daycare who had Down Syndrome. My son played with him just as much as other kids, but if the child got more physical, it would make my son back off. So there are still challenges there.
I do stress to my son to be inclusive, and search out kids who may need someone to play with. I don't know if he does this all the time, but I've seen him do it on playgrounds when I'm sitting there watching. Learning more advanced empathy and social skills is a process, and that can take awhile.