Re: TNG: Silent Weapons by David Mack Review Thread (Spoilers!)
I'd say showing that some humans still believe in deities and/or participate in religion goes with the general thrust of showing how humanity has grown enough to at least deal successfully with several deeply-rooted flaws that remain. It's a more realistic angle on Trek's optimistic view of the future - there's the simple version where humanity has generally just improved, and the more nuanced view where it has grown up enough to deal with internal strife in a constructive manner on a species-wide scale. Realistically, there's just relatively little hope of abolishing religion in the time frame we're speaking about. It's a powerful meme, and recently there seems to be some scientific basis to at least consider that a large percentage of the population may be psychologically set up to gravitate to such ideas.
I'm an atheist, but at the same time the lack of religion in Trek always bothered me. I've always found it hard to believe that religion would just disappear like Trek says it would. I've also never been real fond of the idea that religion was something bad that we had to move beyond. Yeah, religions have brought about some bad things, both now and in the past, but I refuse to believe that they are all bad and that we have to "evolve" past them.
They say a little knowledge is a dangerous thing, but it is not one half so bad as a lot of ignorance. - Terry Pratchett, Equal Rites