hi, here's my 2 cents:
i'm a non-christian, and interestingly enough, i study new testament. i've been to three different institutions in which the intensity of discomfort varied from no discomfort at all (uchicago) to an acute awareness of my distinctly non-christian status (vanderbilt). i think the most honest advice i can give is that in america, you'll continually be reminded of the fact that you're not christian. nevertheless, i think that most schools (liberty, oral roberts, and similar exceptions notwithstanding) rather dig having a non-christian around. even at the uber-protestant vanderbilt, most of my discomfort originated from the fact that my colleagues were all aware of my non-christian religious affiliation, and therefore expected me to give a general "hindu" opinion on a number of christian theological precepts and the like. on the whole, they never tried to alienate me intentionally, but rather, they were fascinated and curious. i found plenty of people to hang with after class, and never had a problem with my social life. i will say that i felt rather tokenized by the administration though (even at such a liberal institution). they liked having a non-christian student in religion, but they never gave much thought to my concerns on a deeper, philosophical level. at uchicago, i felt no such discomfort from either administration or students. frankly, they didn't care about anything other than my intellect (or lack thereof). in short, different student bodies care about different things. also, if you're not in religion, you might not be confronted with others' (and your own) religious affiliations so much. i don't suspect your vector algebra class will care if you believe that jesus christ is your lord and personal savior.