The military isn't a political entity. You don't "clean out" the ranks when the political party that holds the presidency changes. As a vet it irks me when I hear folks complain about this general being a Clinton appointee. Do you realize that it takes decades to grow a general? You just can't pick and choose one out of the blue. They have to come up through the ranks. I came in under Reagan and retired under Bush II. Military professionals don't serve one administration then get out until another one of their liking comes on board. The military serves the country not political parties.
So Wesley Clarke became supreme NATO commander on his own merits?
While the military may rationalize that it's serving the country rather than a particular political party, it serves the policies of the party in power. The country did not elect clinton to go to war in the Balkans and bomb Serbia. However the military carried out those policies.