It could also be a fungal infection. If you have traces of yeast infection in your vagina, he could be having a reaction to it.
could be anything from friction burn, dermatitis, irritated hair follicles, and the list goes on. i agree with vance that he should see a dr. the next time the bumps are visible to get a proper diagnosis, but you can be confident that this is not an std.
It's not a STD, best advice is to see a Dr when it happens to get a proper diagnosis.