Does religion have a place in the armed services?

When America was founded, it was the first secular nation in the world. We not only refused to establish a state religion but explicitly prohibited the government from doing so. Our founders created a living document that allows us to change and progress, to incorporate new ideas, and to ensure that all citizens are given equal protection under the law.
Althroughout history and unto this day we see people hide behind their religion to justify their intolerance and bigotry, going so far as to claim a monopoly on truth and morality, only to perpetuate the biggest lies and perpetrate the biggest atrocities in human history. I believe our founders were right to keep our governing body separated from such pitfalls (since we know it has plenty already), but it seems there are those who disagree with these ideas and wish religion (specifically, theirs) played a more central role in our goverment and in our armed services. I have served with Christians, Catholics, Jews, Satanists, and Jedi Knights, as well as followers of Odin, and I do not begrudge them their beliefs one bit, so long as they are able to perform their duties. It is when religious faith threatens mission readiness that I begin to question its place within the armed services. This may sound overly PC, but as an athiest I feel ostracized when I find out just how deeply religious most of my peers, superiors, and subordinates are, which only becomes apparent when our chaplain comes around. I had a lengthy theology debate with my former CO once he found out I was an athiest, and while it never went beyond that (since he was already leaving the unit) I still walked away feeling like I didn't belong, or that further reprocussions could come as a result. In the hallways I hear people talking about me being an athiest, and it makes me wonder how much those soldiers will trust my leadership with that knowledge. Most of all I am left wondering what place religion (or God, for that matter) has in the military. We serve a secular government, with no religious test held for office, shouldn't the military be a "religion free" zone? If not, shouldn't we open the chaplaincy to atheists and religions that currently have no representation?

Note: Image added by RP Admin