Ed Brayton makes a good point:
I do believe that most military chaplains would be more than willing to counsel atheists as they would anyone else and I don’t think most chaplains are hostile to atheists or to atheism. But even the most liberal chaplain is going to have a very difficult time providing meaningful dialogue that might help a soldier cope with a situation because they start from entirely different sets of beliefs. That’s the same reason why they have chaplains of faiths other than Christianity available to non-Christian soldiers.
If atheists in the military are looking for fellowship & guidance, the military should do all it can to accommodate them.