sex is about intimacy. about dropping pretenses and distractions and emotional and mental protections and trusting the other person. taking off your clothes is the perfect metaphor for all that stuff, and that is pretty much how the mind handles it.
but, intimacy is also everyone agreeing that an experience is intimate. if you are naked, ore often, around other people who are naked, more often, then the novelty wears off and you figure out that nudity is not intimate. seriously, try to get a tomboy to wear a dress. she will freak out like she is completely naked, despite wearing normal girl clothes. it is something you have to get used to