I just started reading all the buzz about atheist chaplains. At first, I didn't know exactly what was being proposed. After a little research I got to the bottom of this weird sounding phrase.
It looks like atheist soldiers are pushing to get an atheist in as a member of the military chaplain program. You can read more about it in this article in The New York Times.
Apparently, while 70% of US soldiers identify as Christian, 90% of military chaplains are Christian. There are a few Jewish and Muslim chaplains, a single Buddhist chaplain and a few chaplains of other religions but the largest single minority in the military, those unaffiliated with any religion, is not represented at all. Having a non-religious chaplain to talk to, especially in the evangelism ridden setting of the US military, would probably be of great benefit to those unaffiliated soldiers.
To be clear, chaplains are not called "Christian chaplains" or "Jewish chaplains" or "Muslim chaplains" so the appellation "Atheist chaplain" is a bit odd. However, I think I understand why it is being used in this case.
I think that use of the term atheist chaplain is intended to get people talking. It's working.
Atheist billboards and bus ads have started dialogues about acceptance and tolerance of atheists in the general population; use of the term atheist chaplain is starting a dialogue about doing the same in the military.