I think that might be difficult, since you have to be ordained within your denomination in order to be considered to be a chaplain. I don't know if the Freedom From Religion Foundation has got to the point where they ordain atheists: it might be profoundly against the point.
Although the Flying Spaghetti Monster crowd would probably start ordaining people if there was enough interest in it within the military.
I think being a chaplain in the military is a very challenging job — meeting the requirements of the denomination as well as the requirements of the military, while preaching a prophetic call could sometimes be at odds with each other.
But as there are more and more atheists in the ranks, it will be something the military should consider.
Anna Marie Martin has been a Spokanite since December 2006, when she moved here just in time to experience some of the worst snowstorms in recent history. She dislikes snow (hate is a really strong word). She grew up in Nebraska, and therefore has no need to be exposed to neither more snow nor more football. Yet, each of these happen every fall and winter, she says.