With the many religions of our Earth (not counting alien words from the series), I really don't think a chaplain is a good idea. The federation is built upon diversity, and it is built on science, and the religious views are left for the characters on a personal level (Chakotay, Kira, Tuvok and so on) and that is good so. A general religion chaplain would not work, and anything else, like a particular religion chaplain would only spark debate, and would be unfair, also introducing some controversial element in a Star Trek series. I really think Star Trek handled religions correctly and as Gene would have wanted until this moment, and I don't feel the need of a chaplain at this point or ever, especially some Earth based religion chaplain, because in that moment they would compromise the integrity of a Star Trek show. Star Trek was never about religion, especially Earth religions and I never ever want to read on forums discussion about contradictory dogmas, like why a Catholic, Baptist, Lutheran or any other religion chaplain said that or about his views/help on a story and so on ... It would really really annoy me a chaplain as main character.