One of the things I hated about TOS, TNG, etc was while the other species have centuries of culture, humans had none. Maybe it was Shatner's vision: Earth had a cultures 'reset.' Humanity became largely docile. Starfleet seems to be for those who didn't quite fit in, but even those humans abandoned history as abhorrent. Most enjoyments were alien in origin. Pets were imports from another planet. No one played basketball or soccer, two games that should be easy to export to starships with artificial gravity. TOS used history for morality plays but never tied it to their present day beyond "oh there was a nuclear war.' Yes TNG had poker. Riker was into jazz, but who else? Secular Humanism as depicted in Star Trek was pretty sterile, and civilizations are never that clean.
As for this view on atheism, it's the same sterility mistake. Being Atheist doesn't mean you worship science. Being a scientist doesn't eliminate your ability to appreciate spectacle, beauty, art, or music.
Being an Atheist doesn't protect you from false beliefs. There are Atheists who prefer anecdotal evidence over rigorous scientific testing. They follow politicians as if they held the keys to enlightenment. They may look the other way when a professional athlete slaps his wife around or destroys a drive through window because he didn't get his hot sauce.
Even Spock required regular pon farr.