Not full-blown rationalist fiction, but I would like to mention The Salvation War (an ongoing trilogy of web novels) as promoting some rationalist values. It's military fiction in which Earth is invaded by the legions of Hell and musters its armies to defend itself. Since it is set in the modern era, there is a fair ammount of focus on science and evidence and the rejection of faith and dogma, and how humanity's curiosity and knowledge led to it gaining power in the form of technology and engineering. Sample passage below (note, "<X>" is a character's name, which I have removed for the sake of avoiding a spoiler).

“As I said, it is what Yahweh and Satan both said. Why should they lie? They are Gods, they demand faith,”
“And I’m a General, I demand firepower. And we’ve seen what happens when your faith meets my firepower. The truth is <X>, you don’t know any of this. You’ve got no proof for any of it. You’ve been sold a bill of goods, just like we were for so many thousands of years. You’ve been fooled, just like we were.”
<X> stared at the pictures taken by the RF-111C, thoughts churning in his mind. He’d never thought this through before, those to whom he owed allegiance had demanded he accept their words and he had. But now he owed allegiance to humans and humans demanded proof. Those were their eternal replies when somebody claimed something. ‘Prove it.’ “How do you know?’ ‘What’s your proof?’ “If you can’t prove it, then it isn’t so.’ And the answer he could give to all those was ‘I can’t.’ For everything he believed was unproven. And that meant so many things.
<X> spoke very slowly as the words formed in his mind, breaking the mental blocks of millennia. “No, I don’t know any of this. I just believed it. And if my belief was false.” His great clawed hand waved over the pictures. “Then all of this, all of it, was for nothing.

Armageddon?

Pantheocide