Not addressing anybodies specific point other than the general one about atheism.
Gene Roddenberry, writing in 'The Making of Star Trek' (page 40):
Eugene Wesley Roddenberry wrote:
Intolerance in the 23rd century? Improbable! If man survives that long, he will have learned to take a delight in the essential differences between men and between cultures. He will learn that differences in ideas and attitudes are a delight, part of life's exciting variety, not something to fear. It's a manifestation of the greatness that God, or whatever it is, gave us. The infinite variation and delight, this is part of the optimism that we built into Star Trek.
This was the Roddenberry of the 1960s. It sounds to me like what he advocates isn't that humanity don't believe
in God(s), but that nobody actually cares about other people's belief systems anymore. Humanity has moved beyond the point where they start conflicts based on one faith or another, and they all respect each others right to have whatever beliefs they want. Some of them probably don't believe in God, while others probably still do. But they aren't hung up on the emotional ramifications of it. They accept and respect each other.
I do think by the TNG era Roddenberry had definitely developed a much more staunch opinion that religion would not
survive in the humanity of the future that he had envisioned, and occasionally TNG/DS9/VOY reflects on that. But it sounds to me like he wasn't actually dismissing
religions in the above quote... he was just saying that the people on the original Enterprise feel comfortable enough with who they are that believing in one faith or another, or indeed not believing in a God at all, means nothing to them as people.