Has any one ever been passed over for a promotion at a civilian or military job because of you non religious beliefs .
No but then again none of my employers or clients have ever had the slightest idea what my religious beliefs are, and have never asked.
I've heard that down in the depths of the Bible Belt (basically, the US Deep South) people have a way of ferreting this out of you, there's a lot of social signaling around who goes to whose church, etc. But in saner parts of the country the topic never comes up and it would be gauche to bring it up.
Currently my main / gravy train client is run by a conservative Catholic and an evangelical who home-schools his children so I consider discretion the better part of valor. I've been with them so long (what, about 10 years now I guess) and they trust me so fully that I think the business relationship could survive such a revelation. But I'm not about to test the theory.
I'll say the military doesn't care anymore. I ranked up at the usual pace and we wore our religion(or lack of) on our dog tags.
I'd have to say no because I've never worked in a place where I was asked about my beliefs and if I was asked I'd likely ask why they needed to know and point out the law to them.