Michael Martin (atheist philosopher) supposedly wrote a fiction book that (if memory serves) featured an atheist protagonist. I haven’t read it though.
Well, that was the non-omniscient main character’s view, anyway. We don’t actually have the proverbial Word of God that that was so. And it wasn’t total sensory deprivation, anyway: The souls in the afterlife were certainly allowed to communicate with each other.
There’s no evidence that it was supernatural. I don’t think that most people would think that, say, a bunch of alien scientists in a lab in another universe qualify as God.
The Fountainhead
Atlas Shrugged
A Brief History of Time
Later Trek’s use of the Prime Directive indicates a theistic worldview, even if they don’t label it as such. Think of every time someone argues that saving some villagers would interfere in some unknowable cosmic plan.
Harry Harrison’s The Streets of Ashkelon is kind of the ur-example of this. It was specifically written as a story with an atheist protagonist whose stance is justified by the events of the story, and was written at a time when that was basically unpublishable in the American market.
Harrison himself was a staunch atheist, and you can usually assume his protagonists are atheist by default unless otherwise stated.
From what I recall, Rand’s philosophy of objectivism includes a sizable dose of atheism as part of its foundation. Not that she beats you over the head with that aspect in her books, but it’s in there if you look closely enough.
The entity or entities involved in Contact had the power to manipulate not only this universe’s physical laws, but even our mathematical laws as well.If entities capable of that can’t be called “supernatural”, then the word has no meaning.
Rand never considered atheism to be a part of Objectivism’s foundation, but a necessary by-product of her metaphysics and epistemology. That is, if you accept the law of identity and the primacy of reason, atheism would be a logical conclusioin.
One of my favorite Rand quotes is: “God knows, I’m an atheist.”
William F. Buckley Jr., a Catholic who preferred the Latin Mass, once wrote that Rand used to scold him, “You are too intelligent to believe in Gott.”
The Dispossessed by Ursula LeGuin has a whole culture of non-believers presented in a sympathetic light. The book is a thought experiment in how an anarchist society could possibly function. I think Shev, the protagonist, first encounter religion when he visits another planet (its sci-fi, obviously), and he is politely puzzled by it.
I dont know if this really fits the OP, but Ged in the Earthsea Trilogy goes on spiritual quests that do not reference God in any way. And in The Tombs of Atuan he tells Tenar that her gods might be real, but they are not deserving of worship. The Old Gods are nothing like a Christian god, though, if thats a requirement.
Pretty sure that Lazarus Long in Time Enough for Love is an atheist, and there are almost certainly other Heinlein characters as well. Maybe Jubal in Stranger in a Strange Land.
It is awfully hard to imagine one of Heinlein’s self-insert characters believing in a power higher than himself. 
I’m pretty sure that Lazarus Long is open to the notion that there might be a God or gods, but his first reaction on meeting one would be to punch it in the nose.
I would go with Arthur C. Clarke’s The Songs of Distant Earth. The novel is a bit of an odd duck, really. In its temperament, it is almost the science fiction equivalent of a “cozy.” The plot and the characters are subdued, everyone is very rational, and while there are things at stake, it hardly feels like the stakes are in jeopardy. This description might lead one to think it is a boring novel, but it isn’t. It’s overall calm, reflective of its characters’ weariness or innocence. There is much talk throughout about how religious belief has long since been abandoned (though one of the main characters is a Christian, and even he ponders why he goes on believing) and religious thought itself is likely just to cause needless problems. Above all the novel is a meditation on time and the cycle of life and death, written from the standpoint of very mature people.
You might look up Garth Ennis’s graphic novel series Preacher. Fair Warning: It’s pretty intense!
G. K. Chesterton’s story The Blast of the Book is about an agnostic professional skeptic and a Catholic Priest who are investigating a book that is supposedly cursed. I’ve linked to the full text. Highly recommended.
Atheism in the Preacher universe would be pretty silly.
Misotheism, on the other hand, would be entirely reasonable (and rather describes the protagonists’ attitude).
Jill Paton Walsh’s Knowledge of angels is about belief and atheism. The atheistic protagonist is from some tolerant, enlightened place that seems pretty utopian from what he says about it, and is stranded Europe in the fifteenth century.
The protagonist in Connie Willis’ Passage researches near death-experiences. Here she’s talking with one of the book’s heroes, a child who’s waiting for a heart transplant:
Somewhere in Bujold’s Sharing knife series, Dag tells a story he learnt about how the gods left Earth after humankind messed up, and will return when people have fixed things. Fawn asks if he believes that, he replies (quoted from memory):
He does complete the sentence with “… we find the One quite adequate,” though.
Of course, this may have less to do with Roddenberry’s vision of 23rd century humanity and more with the episode airing in primetime US network TV in 1967. “Yessir, hail Caesar, sir!”
What if it’s like “The Last Question,” and the universe was… …recreated by an immensely powerful machine intelligence after the destruction of the previous universe?