J.D.
N.,
We all have pre-conceived expectations about how gender affects attitude and bahavior, but it doesn't always come through that way. There's a great book out call "Why Gender Matters". It discusses differences in learning styles, play habits and personalities between boys and girls. There is a section in the book all about boys who don't fit the pattern. This book claims that about one in ten boys are more like your son. It's not about upbringing, or orientation, or any of those things, sometimes boys are just more sensitive and less aggressive than we expect them to be, and it's just who they are. Please don't expect your son to be a certain way based on boy or girl, because it's not always true.
That said, there are ways to encourage assertiveness and self-defense that will work for either gender. Try to give him the words to use. Coach him in the situation to tell the aggressor "That hurts! Please don't do that." Or something appropriate for the instance. At the beginning, you may need to hold his hand and say the words on his behalf. Stress that it's okay to tell someone not to hit or hurt him, and he won't get in trouble.
You might want to try involving your son in confidence and self-esteem building activities. This may sound unorthodox at his age, but have you considered martial arts classes? I suggest this for a few reasons. Discipline is rigorously instilled in these classes, so you don't have to worry that you will have problems with him hitting other kids inappropriately. Martial arts is a non-team, primarily non-competitive sports program that can build confidence and self-esteem through experiencing success. Feeling good about himself and feeling in control of his surroundings should lead your son to feeling more willing and better able to defend himself when he has to. Keep in mind I am not talking about defending himself physically. That's not the goal. Even walking away from a situation because he chooses not to play with someone is a world away from running to cry on Mommy, and it affects his self image differently.