Shaolin Buddhism

When we were discussing the ways of Buddhism in class last time, I was thinking about something within their rules. One of those rules is that one must not harm or kill any sentient being. But Shaolin monks are Buddhists, why do they practice an art that is focused on harming others???

I then went into a little further research on the net and found that Bodhidharma, an Indian Buddhist, went to the Shaolin temple to introduce to them martial arts due to them being out of shape. This then became known as kung fu. I'm kind of confused on this though. If you are supposed to not harm or kill any sentient being, then wouldn't using martial arts against someone hypocritical?

I don't know the depths of Shaolin Buddhism, but on the surface it just seems like it's a little hypocritical to see such peaceful connotation in Buddhism, yet see these guys practice martial arts. I don't know, maybe a lot more further research would clear my confusion just a little...