Ahem, what did you say your street address was, Jenn?
Just kidding, of course.
Correct me if I'm wrong, but does the bible not tell us that Adam & Eve's eyes were only opened to their nakedness after sinning by eating the forbidden fruit? (That's a bit of a non-sequitur for me...) Their nakedness caused them shame, which they solved by wearing fig leaves. So, Ed's theist wife could take the bible-approved route, and just wear one or more fig leaves. Sounds a tad uncomfortable, to me, but then god never did worry too much about our comfort. And no cheating by wearing any other kind of leaves!
So nakedness and shame seem to at least be associated with the Old Testament (which is a bit strange - why would god make A&E ashamed of what he had created - which was, of course, perfect?). The ancient Greeks, who worshipped many gods had no such shame, and nudity was an accepted aspect of their culture. The moslem faith seems to go a huge step further, to the point of completely covering at least the female body with the burkah, exposing only the eyes, although I doubt that this is rooted in shame, in the same way as the bible.
So - nudity seems to have issues that are religious. Maybe atheism's removal of the religious aspects is more likely to create a relaxed attitude to nudity, but atheist = nudist is perhaps taking the correlation a bit far. Atheists aren't all physically beautiful any more than theists are, (myself being a prime example!) so being comfortable nude, even in private, isn't a given.
It would be funny to have her pick a leaf of poison ivy by mistake!!!! :^ )
Outside of the privacy of our own homes, I do think that one's beliefs tend to be one of quite a few determining factors in how much clothing one wears. Behind closed doors though, I would guess that the question of nudity is really dependent upon the individual.
Short of risking heat stroke (the summers here can be brutal), I have always preferred to wear as much clothing as possible, even when alone indoors.
http://en.wikipedia.org/wiki/History_of_nudity is a great read on social non-sexual nudity through the ages and discusses various influences in different places and times.
Of course religion plays a part! It's one of the largest and most pervasive social structures throughout human history. Different cultures had different religions which said many, many different things about nudity. If you mean specifically in the U.S. it will probably depend on what religion you are talking about and which group within that religion. We also get a lot of our "modest" impulses from the British heritage (Victorian era, anyone?) of the nation and the puritan values that spread at that point.
Let's not forget body shame either: if you aren't perfect, you aren't allowed to show too much. Just being larger than you're "supposed" to be makes being naked uncomfortable for plenty of people, at home or not. I was a fat kid all the way through school and lost a good portion of it after, but to this day I still see the "fatty" in the mirror. Shame takes a long, long time to dissipate.