Characters who lack belief are common in SF, yet - unusually for television - they are usually presented in a very positive light. Let's consider a few popular shows.
The characters in the various series are almost universally humanist, and the Federation is almost relentlessly humanist. Star Trek is famous for the sense of hope it conveys about the future, and I think that's largely connected to the humanist sentiment that runs through the entire franchise. In the original series the only main character with any apparent religious sensibilities is McCoy, who does refer to God, and does seem to have a religious background and appears to maintain some level of faith (though he does not appear to be observant of religion). The only main character with any real involvement in even quasi-religious ceremony is Spock, but that ceremony is disconnected from supernatural beliefs. In TNG, the main characters are if anything, more humanist. Worf, while raised by humans, appears to have had enough steeping in Klingon culture to have some degree of acceptance of Klingon religion (he does make reference to Sto'Vo'Kor, for example) and practices some Klingon rituals. None of the humans is particularly religious. Deep Space Nine presents a strongly faith-based culture (the Bajorans), but it is made clear in the show that the beings they base their religion on are not supernatural, simply very powerful aliens.
The captain of the Firefly, Mal Reynolds, repeatedly discusses his lack of belief, and is consequently presented as an atheist. One of the other main characters, Book, is a "Shepherd", a kind of priest, but we almost immediately discover very strong indications that he is much more than a simple priest. In one 'episode' (in both senses) River fixes Book's bible, by removing or changing all the parts that make no sense - the book ends up in tatters. The main "spiritual" character is Inara, her religious sensibilities are more Eastern, and several times she is seen to minister to Book; to my recollection, one episode ends with what can only be described as a kind of benediction - Book kneels before her in misery while she places her hand on his head in a metaphorical blessing. Religion may be somewhat important in the wider culture (it features in several episodes, but is as frequently a source of hatred and manipulation as much as comfort), but it is not important in the lives of most of the most of the crew. A sense that people will be good or evil with or without religion clearly comes through. Firefly is somewhat more independent and libertarian in sentiment than the other shows, but many of its characters have a strong humanist bent.
This show is unusual in that it's an overtly religious society, though many characters are not particularly religious (and a few are openly doubtful). Doubters are not regarded as "evil". Religious and nonreligious characters generally seem broadly accepting of each other. The main religion of the humans is polytheistic, that of the Cylons is monotheistic. Several humans become much more religious over time, but one is of dubious sanity (starting out sane and atheist and becoming apparently insane and somehwat religious); in each case the increase in belief is associated with apparent evidence consistent with that belief (even though some of the resulting beliefs are contradictory).
Stargate is another overtly "humanist" program, but it is much more explicit in its treatment of religion. There are three main "enemies" in the series - the Goa'uld, the Replicators and the Ori. The first and last are gods to their followers - false gods, but gods with great powers nonetheless, so it is little surprise that they have great followings. The heroes aim to convince their followers that those they worship are not gods, and ultimately to defeat the false gods. None of the main characters are religious (though Te'alc is initially a believer, he throws off his religion). The Ori in particular, mirror the worst aspects of fundamentalist, dominionist religiosity.
The Doctor himself is an avowed lover of humanity, and the show is unremittingly humanist. Religious themes do come into the show sometimes, but the explanation is generally more on the natural side than the supernatural.
All of these programs deal in some way with "constructed families"; Firefly is probably the most explicit of these, but in each of them, "family" is something you make, not somethng you are. 'Traditional' families are not a major aspect of any of the shows (on DS9, Chief O'Brien has a 'traditional' family ... and marriage problems); one parent families are common. Yet love and loyalty to friends and colleagues run very strongly in all of the programs. All four show quite clearly that morality and religious belief are largely orthogonal. Stargate is perhaps the strongest in its anti-faith message (it takes no clear position that all religions are false - but all the religions that have a substantive place on the show clearly are false, dangerous and evil). People who lack overt belief are common, and almost all of them are moral, heroic, loyal, loving... and most of all, human.
Science Fiction, and in particular, TV science fiction - because of it reaching a large and regular audience, has a small but significant influence on our society. Because it is forward looking, the influence is generally strongly progressive, and in the way it presents its major characters, generally presents atheism in an extremely positive way, far out of keeping with the common depiction of atheists in other programmes (who are often presented as cold, abrasive, misanthropic or amoral, when they're presented at all).
Book: What are we up to, sweetheart?
River: Fixing your Bible.
Book: I, um... What?
[River is working on a mangled bible. Passages have been crossed out or corrected. Loose pages lie about.]
River: Bible's broken. Contradictions, false logistics... doesn't make sense.
Book: No, no. You - you can't...
River: So we'll integrate non-progressional evolution theory with God's creation of Eden. Eleven inherent metaphoric parallels already there. Eleven. Important number. Prime number. One goes into the house of eleven eleven times, but always comes out one. [She looks him in the eye.] Noah's ark is a problem.
River: We'll have to call it "early quantum state phenomenon". Only way to fit [laughing quietly] 5,000 species of mammals on the same boat... [She rips more pages out.]
Book: River, you don't... fix the Bible.
River: [Speaking gently.] It's broken. It doesn't make sense.
Book: It's not about... making sense. It's about believing in something. And letting that belief be real enough to change your life. It's about faith. You don't fix faith, River. It fixes you.
(Book tries to pull some of the ripped out pages from River's hand, but they tear.)
Book: You hang on to those then.