It's not that the jury ruled for self-defense. Self-defense was just the reason given by Zimmerman for why he killed Trayvon. But the burden was on the state prosecutors to prove
beyond a reasonable doubt that the death of Trayvon " ...was caused by a criminal act “demonstrating a depraved mind without regard for human life."
(Source)As per the verdict, the jurors doubted that Zimmerman committed the killing in a manner consistent with second degree murder. Therefore, he was found not guilty of the charge.
Sunset, although the jury did ask for clarification, the court said it couldn't provide an answer based on a general question, but only specifics. The jury never responded back with a specific question. In context of how the verdict came out, I'd say all the jurors had doubt on the second degree murder charge and most were looking to decide not guilty. The question may have arisen from just one person holding out wanting the group to consider manslaughter. In the end, I think they just wanted to address the single charge that the state brought forward rather than help the prosecutors.
Personally, I think the jurors made the right call. Zimmerman did not murder Trayvon. Both of them acted wrongly. Zimmerman probably shouldn't have tailed Trayvon and Trayvon probably shouldn't have gone and confronted Zimmerman. At the end of the day, Trayvon is dead. There is no perfect justice to resolve this situation.
Of course, this isn't over. There could still be a civil trial just like in the OJ Simpson case and federal civil rights charges. It ain't over until it's over. But in terms of this part of the case, the right decision was made.