President Bush typically got quite warm and favorable responses from the troops during his tenure, which I find puzzling, as it was his administration that didn't supply the body and Humvee armor needed until it became a scandal, required multiple rotations of duty in active war zones with little time off, treated returning wounded veterans rather shabbily. I can only guess that his popularity was a personal popularity, i.e. he was popular because he was George Bush, not because he was Commander-in-Chief. I think perhaps they saw him as George W. Bush, a man of stated American values, ideals, and visions; traits that are highly regarded and shared in the military. Plus, he had served (to some degree anyway) in the service himself, so they may see him as "one of their own." And finally they may have seen him as tested by 9/11 and not found wanting (at least at that point in his Presidency). Personally, I think President Bush let them down, but apparently these troops at least don't agree. I wonder what they'll say 10 years from now.
To be fair to President Obama, he's new and untested and unknown. Naturally they're not going to give him the kind of ovation they gave President Bush. He's the antithesis of much of the above. Though the unusually lackluster response was, I thought, bordering on disrespectful. I think this goes to show that a new President needs to win the hearts and minds of his countrymen. He'll get their salute as the President and Commander-in-Chief, but he won't get their standing ovation until he earns it. And Obama has yet to do that with these servicemen. Whether or not he will remains to be played out. For the sake of the country, I hope he does. When a soldier doesn't believe in what he's doing, it's not good.