Atheists, in general, are Liberals (Democrats for all of you not in the States) and liberals are traditionally wary of the armed forces. I get strange looks from many of them when I mention that I consider the armed services to be a rational choice for either of my children to make when they are adults. Is it my first choice? No. Would I be OK with it? Yes. I'm not naive. The military's main role is to kill folk. Sure, they use Orwellian language like Defending the Nation and stuff like that, but that just translates into killing people or threatening to kill people. We can debate when it's acceptable to kill people and that's one of the benefits of living in a free society. Also, there are many useful secondary missions like nation building and keeping the peace that can only be done by people with guns. That's my current policy regarding the military and my kids.
Atheists are in the minority in our culture. Seeing that atheists are becoming a more vocal minority the armed forces have taken steps to accommodate them. Soldiers can identify themselves as atheists on their dog tags and can have an atheist symbol (the atom) on their gravestone. Obviously, everything is not all rainbows and puppy dogs for atheists serving. There are many stories of individuals facing prejudice. With strong advocacy the culture in our armed services will be more open to non-theists.
Here are some interesting links concerning Atheists in the Military:
Military Atheists Group
Military Religious Freedom
Military Association of Atheists and Freethinkers