How to teach my son that not every dog is a nice dog?

Start teaching him to ask permission first before touching any dogs he doesn't know, or isn't around very often. Good dog owners will not be offended by you asking, and really good dog owners will be honest and tell you if their dog bites or doesn't like children. I know your son is young, but if you start teaching him now that no adult or not asking means no touching he will get it quicker.