Contraceptives came about within the blink of an eye, genetically-speaking. Until a few decades ago, they did not affect selection at all. The ancestors of contraceptive-users might have wanted contraceptives but they didn't exist and so they had no choice.

Now that contraceptives exist, people who choose them and deliberately avoid ever having children will select themselves out of the gene pool. The same goes for people born in religious communities who are skeptical of their religion. The people who remain in those communities will be the ones who have some sort of genetic predisposition to religious experiences. This is already a hypothesis (the God gene [1]).

[1] https://en.wikipedia.org/wiki/God_gene