The courts condemned Zelaya's actions and he wanted to go ahead with it anyways. One way or another, it was likely to become a dictatorship.
I believe in electing leaders through democratic means and updating laws through proper channels. Using a hyped up public to back a move that is not yet considered constitutional (therefore unconstitutional) is not an example of going through proper channels. The public can be all for one thing one moment and all for something else the next. The fact that these things take a long time to change is an advantage. It gives people a lot of time to think about stuff.
Look at our example of intense security. The public was screaming for that sort of stuff back right after 9/11.... they're not so crazy about it anymore. Now they're screaming that it's becoming a police state.
If the military does not cling to power and helps organize another democratic election, it would really save its image. I'm not really counting on them to do it, but I'd rather see a military dicatorship than a Communist dictatorship. The former tends to be more reasonable to deal with than the latter.