To me Star Trek represents (and should represent) sort of evelved humanity that has no use for religion. They solve their problems with reason. Superstition just do not fit that worldview.
... to highlight the diversity of humanity.
In my own mind, the size of the Federation is approximately 800 billion to 1 trillion people, this is the number I use in my head. It is composed of hundreds of intelligent alien species, thousands of worlds and millions of cultures and societal groups.
I could no more conceive of most of them belonging to the same church, than I could most of them being atheists.
The people of the Federation probably have a dizzying number of opinions and beliefs on the subject we've been discussing. Atheism would be a part of the overall mix. This in no way changes the Federation into a theocracy, or Starfleet into a group of missionaries. A Chaplain would one character among many on any new show, he or she would be a difference to what has come before, and a exploration of a aspect of Starfleet and the Federation that we haven't seen previously.
This is Merry Christmas, and I approve this message.