I believe he was shot because he was bashing Zimmerman's head into the concrete.
Wonder why that obvious thought doesn't occur to the persons who automatically assume racism. Actually it appears from the transcript of the call that Zimmerman wasn't even sure of Martin's race when he started following and observing him. He was doing so from a distance at night, and called the police because of what he considered suspicious behavior. "This guy looks like he’s up to no good or he’s on drugs or something. It’s raining and he’s just walking around looking about." (transcript) When asked by the dispatcher, "OK, is he White, Black, or Hispanic?", Zimmerman says, "He looks black." Just looks. He has already called the police, and he's not sure yet of the race.
Later, after answering some more questions, Zimmerman says that Martin is "coming towards me". Only then, after seeing him more clearly, does he add, "He's got his hand in his waistband. And he's a black male." Now he's sure of the race. Before he didn't even know for sure.