I am about to talk over my own head for a moment, so please forgive me (and feel free to correct) if I get a few facts wrong.
I used to love Star Trek. I used to watch it every week in prime time, and even during the late afternoon syndication slot. When the spin-off series Deep Space Nine started up, I watched that as well, and I really enjoyed it. When Star Trek: The Next Generation (hereafter referred to as TNG) ended, my enthusiasm for DS9 waned fairly rapidly and I ended up abandoning the entire universe. And now that I think about it, I haven't enjoyed a sci-fi TV show since then until Battlestar Galactica, which I am just now discovering. I really like Battlestar Galactica. I think it is a fantastically well-written show, full of mystery and drama, almost completely void of cheer and comedy.
TNG was a very cheerful show. Sure there was drama, sure there was danger and even a death or two, but for the most part, it was a very brightly lit series that dealt with exploration and scientific discovery and social progress. DS9, on the other hand, was dingy and gloomy, dealing with terrorism, civil war and religious strife. BSG, incidentally, is similar in tone (although superior in nearly every measure) to DS9, and shares many of the same writers. In a relatively typical TNG episode, the conflict centered around a newly discovered civilization whose progress was being impeded by a clearly false religious belief. The intrepid crew would unveil the conmen or corrupt religious leaders, or explain the natural phenomenon that was causing the misunderstanding and everything was great. In a typical DS9 episode, people died because of the civil unrest on the planet or because of a confrontation with the perpetual villains on the other side of the intergalactic border. A much darker show by all accounts. And here's the thing: Gene Roddenberry, the creator of all three shows, died a short time after creating DS9. He was, famously, an atheist with a clearly positive humanist vision of the future. In Roddenberry's universe, religion is a thing of the past. With religion out of the way, the people of Earth were able to unite and funnel their resources into scientific development. Starships were clean and resourceful, replicating food from recycled waste (this was implied - I doubt if it was ever explicitly stated this way). The exploration was as non-invasive and gentle as possible - phasers were always set on stun and the Prime Directive insisted that the development of 'immature' societies would not be interfered with. The show was bubbling with optomism and hope. The plot of DS9, on the other hand, was tethered to an outpost on a planet run by religious zealots - I always assumed it was some sort of allegory for the Arab/Israeli conflict. BSG is also heavy with religious overtones - I am just starting season 2, so I don't know where they are going with it all - no spoilers please!
It is tempting to think of the latter two shows as 'more realistic' than the first, and perhaps it is. But that is because we live in a world that is overrun with religious warfare of one kind or another. The happy, hopeful universe of TNG seems as unlikely and far off as that of The Jetsons. BSG and DS9 may be more accurate reflections of our society - if a galaxy-trotting, alien-shooting show can remotely be considered a reflection of anything we have here in the first half of the twenty-first century - but in my mind, that only makes Roddenberry's TNG universe so appealing and tantalizing. The TNG universe is a glimpse of what might be if there were no religion. The BSG universe is what might be if religion continues to dictate our lives. Those deists who say that atheists live hopeless lives are fools. The atheist (freethinker, humanist, bright, agnostic, etc) has days full of hope, but is tethered to the inevitable despair of a world saturated with religion. We want to develop new technologies, we want to spend billions of dollars on science instead of war, we want to be free of the fear of terrorism, but we can't be until Christianity and Islam drift into mere folklore and superstition.