Very normal behavior autistic or not. My daughter started at 2 and stopped recently. I was a single mother with no men around and there was no way anything happened to her she just liked how it felt. It was uncomfortable for me to see and there were times that she would just drop on the floor and watch TV and start doing it. I found that she was very high energy and it seemed to calm her down in a way.
As long as he isnt doing it in front of people and he does it in his own room it is fine however I would talk to him about it not to make him feel ashamed but to make she he understand that it is a private thing that is done in the bedroom with just him not at school etc.
That is what I do. I used to joke around with my daughter about it because I didnt want to make a big deal about it, that is how I dealt with it :)
It's normal for any boy of any age to play with his penis. This has nothing at all to do with autism. I'm actually impressed that he does this in the privacy of his room, since a lot of kids on the spectrum lack the social awareness that some things are best done in private. He's a normally-developing child in terms of what you're describing.