Zimmerman had not directly confronted Martin at the end of his 911 call. (Q: How often does someone contemplating murder call 911 first?)
Once the 911 call ended, we have no actual evidence of what was happening until an uninvolved eyewitness saw Martin beating the snot out of Zimmerman - a beating that only ended with a single gunshot. Zimmerman's story - admittedly uncorroborated - is that he was returning to his car when Martin circled around and attacked him. Local, state, and Federal law enforcement haven't been able to punch a hole in this story. Unless you think a doofus like Zimmerman is actually a genius criminal mastermind who can fabricate a consistent story that holds up to that level of scrutiny while suffering from a bloody head and nose (not to mention the adrenaline dump of being involved in a shooting), maybe he's telling the truth.
There's lots of inference, speculation, politics, and downright wishful thinking surrounding this case, but given the absence of actual, hard evidence (eyewitnesses, security cam footage, forensics, etc.) contradicting Zimmerman's story, there seems to be an abundance of reasonable doubt in regard to the charges.