I remember hearing that, if you examine tapes closely, during every administration, that, before the President exits Marine 1, the Marines face toward the White House until the President gets to the steps leading down out of the chopper, then they turn in and face toward the steps. Not so during the Clinton administration aberration, I've heard but never confirmed. This is an urban legend. Regardless of how the individuals of the military felt about clinton, and believe me it wasn't much, they would never have treated him with anything other than with the respect his office demanded.
For better or worse, he was the Commander in Chief.