I'm not necessarily saying that we need to deprogram male children. You're right, that would be completely wrong. However...
To me, it appears as if we force many boys to fit into this stereotypical view of men. That if you're going to be a man, you have to act like the stereotype. You have to be violent, you have to be aggressive, and you have to be dominate over women. Our society is set up in such a way that a white man (who I am myself) is the ideal person. Yes, women have gained rights, but how do we make the world even more fair for women? We treat them as if they were white males. They don't get these preferences because they are human, they're given these preferences because they aren't white men. To be a man, is to have power.
I'm not saying we need to get rid of things that perpetuate male stereotypes, but if we're going to show them to kids (boys in particular), we need to educate them at the same time. If we let Rambo and James Bond play father for our boys, we're going to end up with little Rambos and James Bonds.
I'm not saying we need to 'change' boys, but rather educate them in the differences between men and women (because there are plenty), and erase the stereotypes that men are dominate over women.
Now, most well-adjusted men in the world (be they the stereotypical male or not) will not rape a women. So where do those who do, come from? I couldn't tell you the answer, but I'd speculate that it's men who've grown up as boys trying to perpetuate the male stereotype. They want the power, they want to be dominate over women, but for some reason they aren't. So to get that power, they rape.
Rape is a crime of power. We teach our boys that men are powerful, and dominate to women. That is inherently wrong. I'm not saying to get ride of violence, James Bond, or anything like that. I grew up playing with toy guns and GI Joes as a kid, and I've turned out fine. The problem is, not everyone does. And because of that, people get hurt.
Educate men on rape prevention. Teaching women self-defense is just reinforcing the idea that it's the woman's fault if they get raped, because she didn't prevent it.