Okay, first things first: the fact that most of the Iraq/Afghanistan movies released in the last few years (Home of the Brave, In the Valley of Elah, Lions for Lambs, Redacted, Rendition) have been flops or disappointments doesn't mean that the American public is implicitly rejecting their criticism of the Bush administration's military and foreign policies (the polls on those specific subjects are proof of that) any more than the disappointment of, say, Amazing Grace means that people are now in favor of slavery. The American public is preferring to choose apathy over the tension of current events with their hard-earned movie dollars.
One of the reasons for the lack of interest in these kind of movies is that we're still mired in Iraq. Audiences need time to decompress, and filmmakers need time to gain perspective. Stop-Loss, like DePalma's Redacted, is so in-the-moment, so angry and passionate (in different ways) and so intent on doing something, anything, dammit, to Make A Difference, that good art gets lost in the process. Director Kimberly Peirce makes two crippling mistakes in Stop-Loss: She makes a self-consciously political movie at the expense of characterization and story, and the political points she makes are, in a word, clumsy.
After wrapping up a bloody final mission in Iraq, a bunch of soldiers head back to a homecoming in Texas, only to be met with mental illness (everyone has Post-Traumatic Stress Disorder), physical decrepitude (one guy has been blinded and lost two limbs), and, worst of all, the news of forced re-enlistment. Now, the existence of 'Stop-Loss' programs aren't news to me, but when Ryan Phillippe arrives at the movie's titular scene, he basically throws a tantrum, outraged in a way that only somebody who's kind of ignorant about the world around him could be - that's not the character's fault, that's the screenwriters' fault. If the movie ever explained the deeper roots of the military's enlistment problems - our overextended armed forces, our pathological desire to avoid a draft, etc. - it would have provided a useful context for a political discussion and, ideally, dramatic complication. But since Peirce doesn't go there, the effect is to make Phillippe's character look self-absorbed and dumb. Add to that how clumsily she handles the rest of her drama (the scene in which Phillippe visits his wounded, one-armed comrade in a hospital is laughable) and you have a movie that, duh, people aren't going to want to see.
I'm being too harsh, because the movie isn't a total turd - it halfway works thanks to a sense of genuine outrage and frustration, and decent performances - but when you're working with a subject this charged, halfway just isn't enough these days.