I try to avoid second guessing juries, even when they don't come out the way I might think they should. And I generally would not say that any acquittal in the criminal justice system shows that the system is not working. That's because our criminal justice system is supposed to be based on the premise that it is better that ten guilty men go free than that one innocent person is convicted. A wrongful conviction might be used as evidence that the system is not working. But an acquittal, even of a guilty defendant, shows the system is working the way it was designed.
What happened to Trayvon Martin is tragic. But it was always a difficult case to prove beyond a reasonable doubt, which might be one reason the Florida prosecutors initially did not want to pursue it, until a public outcry forced their hand. In addition to the ambiguities and conflicts in testimony that make it difficult to determine exactly what happened, the case also exposed deep divides in the way people perceive dangers, in the way we decide who to empathize with, and who we fear. If you're George Zimmerman, a black teenager wearing a hood is probably up to no good. He's the "other." If you're Trayvon Martin, an armed neighborhood vigilante is someone to be feared. If we were instead talking about a white teenager being stalked by an armed black vigilante, many people's perceptions of who is one of "us" and who is the "other" would change.
I saw a video recently in which a news crew placed a series of actors in a park, each very obviously trying to steal a bicycle by using wire cutters to break the lock. When the thief was a young white kid, hardly anyone bothered him. When it was a black kid, people aggressively interfered and called the police. And when the thief was an attractive young woman, men actually stopped and offered to help! To the extent these kinds of biases caused Trayvon Martin's death, and might affect the way people perceive and perhaps decided this case, it's understandable that the case aroused passions.
But even though we can't help thinking about how this case reveals people's biases, and how the criminal justice system can reflect those biases, it might be more comforting instead to think of this case as another one of those high profile trials in which the defendant, with the assistance of well prepared counsel, is able to get off. In the long run, those kinds of cases don't say as much, fundamentally, about our justice system as people think at the time.