Some military religious freedom organizations are raising the alarm about growing hostility toward Christians and chaplains in the military.

Several recent incidents suggest that openly practicing one's Christian faith is resulting in discharges and punishments.

Washington Times:

Christians are leaving the U.S. military or are discouraged from joining in the first place because of a “hostile work environment” that doesn’t let them express their beliefs openly, religious freedom advocates say.

Michael Berry, senior counsel at the Liberty Institute, a Texas-based legal organization dedicated to defending religious liberty in America, said recent high-profile cases of military chaplains facing punishment for private counseling sessions that reflected the teachings of their religion could cause devout Americans who are qualified for military service to think twice about joining the military.

In December, a chaplain for a Ranger training battalion received an administrative letter of concern after a soldier complained that he advocated Christianity and used the Bible during a mandatory unit suicide-prevention training session. The Military Association of Atheists and Freethinkers said the chaplain “used his official position to force his personal religious beliefs on a captive military audience” in an article the group posted on its website.

And, last month, a Navy chaplain was removed from his post and may lose his career after some sailors complained about his private counseling, in which he reportedly advocated against homosexuality and sex outside of marriage.

Mr. Berry represents both chaplains in question.

Militant atheism is as much of a belief system as any organized religion, so the question is, why doesn't the military treat it as such?  The reason is that the Association of Atheists and "Freethinkers" (a misnomer if there ever was one) is suit-happy.  The military is terrified of seeing itself portrayed as anti-gay or pro-Christian, so it takes the easy way out and punishes soldiers, officers, and chaplains for being too forward with their faith.

“People of faith are going to stay away from the military,” said Mr. Berry in an interview with The Washington Times.

“I can’t tell you how many moms and dads I’ve spoken to who say, ‘My son or daughter wants to join the military, [but] in light of what you’ve described, I’m not sure I want to let them join the military anymore,’ and I don’t blame them. I would have serious reservations about my own kids joining,” Mr. Berry said.

Douglas Lee, president of the Chaplain Alliance for Religious Liberty, whose job it is to find people who want to be chaplains and make sure they’re also qualified to serve in the military, said growing religious hostility within the military is making it harder for him to find potential recruits and for the armed forces to maintain the chaplains it does have.

“I know people who get out, officers and chaplains, who’ve said, ‘I can’t serve the way I want to in this environment,’” said Mr. Lee, who also served as an Army chaplain. “People who’ve said, ‘Because of the religious liberty challenges I see, I think I’ll serve somewhere else.’”

Not being able to recruit or retain these individuals is very dangerous from a national security standpoint, said Mr. Berry, because they could be the military’s next group of leaders, but will never serve because they don’t think they’re welcome.

“We all used to sit around and talk about planning on spending 20 years, but at some point enough is enough,” he said.

There is a lot of anecdotal evidence that this is getting to be a big problem, but there is no statistical evidence to back up the claim that devout Christians are being targeted and are leaving the military in great numbers.  But given how active militant atheists have been in recent years, it's safe to assume that the problem is bigger than it appears and that the military is being cowed by social justice warriors into smacking down any overt display of religious belief. 

Real "freethinkers" could care less about someone's religious beliefs – or at least wouldn't attempt to suppress them.  The success of militant atheists in the military threatens not just the free exercise of religion in the ranks, but anyone of faith who runs afoul of their narrow view of the world.