According to this article by Newsweek, 3,301 U.S. active-duty soldiers deserted the Army in 2006. 

Jeffry House is a defense lawyer representing many of these soldiers.  Newsweek asked House why so many soldiers were deserting.  According to House,

The common idea is that the war in Iraq is going nowhere, and it’s bogus, as I’ve been told [by soldiers] many times. In other words, there was no justifiable reason to attack Iraq in the first place. People are now telling me stuff like, “We clear out a section of Baghdad, hand it over to the government, and the next day 70 bodies would appear.” They feel like they’re helping the Iraqi government, which [they feel] actually is a bunch of death squads in disguise. So they begin to feel responsible. People can’t justify to their own selves what they’re doing there, it just seems wrong, wrong, wrong to them. I have a couple of guys who actually finished a six-year commitment. They were given an honorable discharge. They got nice medals and a nice party, and when they drive up in their driveway at home there’s somebody giving them a stop-loss document, which means you’re back in [the service] at the [military’s] pleasure. People are very disheartened.