Taken from Wikipedia
Traditionally, a chaplain is a minister in a specialized setting such as a priest, pastor, rabbi, imam, lay representative of a world view attached to a secular institution such as a hospital, prison, military unit, police department, university, or private chapel. Though originally the word "chaplain" referred to representatives of the Christian faith, it is now applied to men and women of other religions or philosophical traditions–such as in the case of the humanist chaplains serving with military forces in the Netherlands and Belgium.
I find the idea of a chaplain on a modern day warship ironic. Since most religions at the root of their teachings are peaceful. Its often man's interpretation of the scriptures that leads to war. So why have a person of faith serving on a ship that potentially could bring the deaths of a lot of people? It's definitely not in the ideal of spiritual peace and harmony.
For this reason I think it would be interesting to have a Chaplain who was a non believer in any religion but open minded. Trained to respect and help individuals contemplate their own beliefs. I think a Chaplain with his own strong faith guiding others who worship wormhole aliens and idols etc would have conflicts with his own beliefs too much to be an objective advisor. I think a counsellor is more fitting for this job- assuming they didnt have their own strong faith.