For the record, I recognized immediately that he was trying to slam Bush and flubbed it. It is the most obvious explanation, which we all know is usually the correct one, but man, he sure just kept on digging, didn’t he. He should have just apologized to the troops and not tried to blame Bush. Kinda dumb the way he handled it.
Here you go, Jay explains it.
Not So Fast 
With most people, I’d agree that that would be the most obvious explanation, however given his history of “support” for the troops in vietnam, I’m not convinced.
A third scenario is that he did, in fact, mean to impugn Bush but the fact that this statement actually reflects his opinion of our armed forces made him less careful about his words.
I’d wager on the last one before anything else.
#3 does have merit. I just think he would know hating on Bush is okay and slamming the armed forces is political suicide. Either way, he has handled it poorly. Really, really poorly.