It hasn't, really. Although while stationed in TX, my family's lack of religious convictions was a consistent, though small, thorn in my side. Every person we met invariably started a conversation with "My name's Bill, what church do you belong to? Oh, you don't have a church, you should try mine!" Got old after awhile having that conversation with everyone you meet...but that was largely out on town, not nearly so much in the squadron.
I have honestly never had a problem working with someone in the squadron because of their beliefs or my own lack of them. I've had some good discussions about religion, but all in the same way you might debate politics, or USAF policies, or any of a hundred other things that get debated on a daily basis.