I'm not so sure that in the long run, all of these assumptions are correct, but let's just assume the author is right and due to intractable cultural, biological, and emotional factors, atheists will always be a minority in Western society.
As a member of such a permanent atheist minority, I would be willing to have the same sort of status that Jewish folks enjoy -- tolerated, respected, and integrated into society without needed to be closeted, with only the Helen Thomases of the world doubling down on bigoted nonsense about us, and being roundly condemned from all quarters for doing it. In nearly all segments of polite American society, anti-Semitism is socially unacceptable; it cost Ms. Thomas her job and will likely cost her some public respect and speaking engagements she otherwise would have enjoyed. You don't have to be Jewish to find this sort of thing objectionable. If atheism gets at least that much respect, that would be okay with me.
But as it is, when atheists dare to raise their voices and publicly identify themselves as such, they are met with nonsense like this -- people refusing to ride busses carrying advertisements saying "Millions Of Americans Are Good Without God." Note that the advertisement says nothing negative about Christians or Christianity at all, yet the ministers in the linked video act as though the advertisement were an existential threat. I suppose the Coalition of Reason ought to thank the ministers for reacting this way and magnifying the impact of buying advertisements on four busses -- there's no press more powerful than free press, and had these guys just kept their mouths shut and not sent out indignant press releases, it's likely that literally dozens of people in Ft. Worth would have noticed the advertisements. It's not like the advertisement was at the entrance to the Lincoln Tunnel or anything like that.
I don't see Christian leaders encouraging boycotts of busses advertising Jewish temples trying to attract parishioners for Hanukkah services. Perhaps more to the point, you don't see atheists boycotting busses carrying advertisements for Christian churches. What I do see, though, is that when I get together with my local nonbelievers' group in a public place to discuss philosophy, officious intermeddlers become so enraged out our mere existence that they interrupt our meeting to say that we "shouldn't be saying things like that in public" because it's "rude." (While remaining silent about the Christian prayer group loudly overstaying its reserved time in the room next to us.)
Still, I have some hope that encouraging people to think critically, embrace science, and consciously analyze their morality can, one person at a time and over the course of a long period of time, spread apathy to religion and thus free up economic and social resources for more productive kinds of efforts -- scientific and medical research, building hospitals instead of houses of worship, distributing textbooks* instead of holy books, and holding faithfully to the Constitution -- than the sometimes-beneficial, sometimes-not sorts of social activism coming out of religious institutions these days.
This doesn't mean I want everyone to abandon their religious beliefs; it means they should be free to believe as they wish, or not, as they choose, without significant social stigma. If in such an environment, atheists remain a small minority, so be it. If people make social policy and economic decisions without relying on millennia-old tracts of facially ridiculous mythology like the Torah, the Koran, or the Bible, that would make a better world than what we've got now.
* I've a thought about this subject, too, which I need to think through and may write about later today. That thought will not address issues of religion or atheism, however.