"Captain Jean-Luc Picard. I wish I could say you've been like a father to me, but I've never had one so I don't know what it feels like. But if there was someone in this universe I could chose to be like, someone who I would want to make proud of me, it's you. You who have the heart of an explorer and the soul of a poet. So, you'll understand when I say: death is that state in which one only exists in the memory of others; which is why it is not an end. No goodbyes, just good memories. Hailing frequencies closed, sir."
"Au revoir, Natasha..."
- Tasha Yar, in her recorded message, and Picard's whispered response
These are not people who need chaplains. Even at the moment of death they do not require religious assurances of the afterlife, nor a priest to comfort them.
Now, you can argue that this should be changed, and religion brought back, but personally I'd think this to be a huge mistake. I like them as star faring atheists. I understand that others could have different preferences, but this is my opinion I stick by it.