The hostility toward religion among American intellectuals arises, I think, from a clear awareness that it was against a publicly religious culture that their own culture rebelled. Now that rebellion is completely successful in terms of capturing control of all the public instruments of transmission of culture-- the universities, the media, and the literature and art-- but it has become such a shibboleth of intellectual life to snipe at religion that, like the aging "revolutionaries" of the old Soviet Union, they mindlessly continue to "rebel" in order to defend their tight grip on the establishment. Indeed, those intellectuals are the establishment. And what was once a daring and rebellious stance is now just another example of lockstep conformists mindlessly echoing ideas that they haven't examined.
In our culture, intellectuals have become so uniformly a-religious or anti-religious that our fiction, with few exceptions, depicts religious people in only two ways: the followers are ignorant and stupid and easily fooled, and the leaders are exploitative and cynical, manipulating others' faith for their private benefit.
That's when contemporary fiction mentions religion at all. Most of the time, in and out of speculative fiction, religion simply doesn't exist. Characters don't believe in God or even think about believing in God. Nobody talks about religion. Nobody belongs to any kind of church. Religion simply doesn't exist.
The honest depicter of human life will include the religious aspect of that life. This is not to say that stories need to be about religion, any more than stories about our contemporary culture need to be about cars. But the cars need to be present, at least by implication, and if a character doesn't know how to drive, we'd need to know why.
Card is Mormon, incidentally. Or maybe not incidentally.