I am a Christian. Roddenberry showed a chapel ONCE in TOS, hey I can live with that...his original vision of the future was one where our God (and the human invented ones) weren't a big part of their universe. But by the time Voyager comes around, they've got big chunks of major plotlines using "spirit guides" (which would read "demons" to some of my faith) and the female captain is going all gooey about how cool it is. ROWLS.
Roddenberry showed a Chapel many times in the original series. Heck, he even wound up marrying her.....
You should check out the Star Trek TOS episode "Bread and Circuses", about a world of parallel Earth-like development where Rome never fell, but survived to develop Twentieth Century technology, and still persecuted a peaceful sect of "sun worshippers".
From the Wiki description at http://en.wikipedia.org/wiki/Bread_and_Circuses_(Star_Trek):
"Back on the ship, Kirk commends Scotty. Spock expresses curiosity to Kirk and McCoy as to why the slave "Sun" worshipers seemed to adhere to a philosophy of peace; again incorrectly, Spock says that in most societies sun worship is a primitive religion of superstition, with no philosophy behind it. It is at this point that the landing party learn the true meaning of the repeated references to the "Sun/Son". Uhura, who has been monitoring radio transmissions from the planet, informs them that the worshipers are actually referring to a "Son," rather than "Sun," as in, "the Son of God." Kirk replies in realization: "Caesar ... and Christ; they had them both..."