There are atheists in the foxholes. I have never actually seen the argument that there are no atheists in the military employed in a debate, but I have always found it to be a repugnant one. For one, it has an undertone suggesting that we are cowards, and much more importantly, there are undeniably atheists in the military! Now, according to the article I linked to about, on top of having to remind people that they exist (in greater numbers than military Jews, Muslims, or Buddhists), they receive less support than their brothers and sisters in arms.
Thanks, John, for the link!