you know, i'm one of those guys who's been on flights where people have said thank you, and plenty where people haven't. I personally don't make the "thank the troops" statement when we board, or de-board the airplane, however, if my FO went and did it, i wouldn't criticize him for doing it.
I myself am very thankful for what US soldiers have done over the various generations (this one included). I'm proud to be an american, and seeing these servicemen/women helps reinstil that pride. I do hope that all of them can make it back home, and sooner rather than later. I might be an idealist in that respect, and i may not agree with "what we were told" were the reasons for invading Iraq, but my idea of supporting the troops, is if they're going to be there, lets give them everything they need to win.