We've known this for a long time, but speaking politically, the least popular people in America are atheists. This piece by Max Boot is a recent addition to the discussion. He ably points out the various ways in which atheists are stigmatized in the public culture. And all this despite the claim of many conservative religious people, which is not without its plausibilities, that the public culture is structurally hostile to any expression of "serious religious belief," as I have heard multiple people frame the complaint.
Boot's piece doesn't really go into the history, which is unsurprising because of the manic immanent and imminent ahistoricism of our world--people simply assume every moment is complete in itself and need not be informed by any sort of history. But the truth is, I believe atheists have their distinct stigmatization today because of the past seventy or so years--because of "godless communism." Remember, it was only in the '50s that "In God We Trust" was added to US currency, and "Under God" was added to the Pledge of Allegiance.
Why did those get added then? I am not alone in thinking: because of the cold war. The US had taken upon itself the mantle of opposition to the USSR and the Communist Menace (which I capitalize to belittle our fears, a little bit, but also which I don't hold off at arm's length ironic distance with scare quotes because, indeed, it was a real menace), and because of that polarization, the US was shaped internally in certain ways over decades by that opposition. It is impossible to believe that what Eisenhower called the "Military-Industrial complex" would have arisen, or that it would have captured as much political power as it has captured (and continues to retain), without the arms race. On the other side, the civil rights movement in the US, and all claims towards egalitariaism, were also helped by the US's presumptive claim to be an example of "freedom" for all the world. This book tells that story very well. Public culture in the US was deeply shaped both directly by the threat of communism, and also indirectly by the presumption (our presumption, in the US) that "we have to be better" and more upright. (Whether we were "better" in any sense is another question--the point here is simply the motivation and rationale.)
In light of all this, it's not surprising that the figure of the "atheist" took on a hugely negative valence in American culture over the period 1945-1990. This is especially noteworthy because before that time, atheism wasn't always seen in so negative a light; among the most popular journalists of the pre-war era was H.L. Mencken, whose position on religion is not hard to find, quite far from friendly, and unlikely to land him a spot on the Today show even in 2019. Susan Jacoby's very informative book Freethinkers: A History of American Secularism is a terrific survey of some of the history of this (though she is sometimes an axe-grinder, and very definitely has a pony in this race).
So what this tells us is: the public culture of an age is, as it were, "structurally isomorphic" to the context in which the society that hosts that public culture finds itself. That culture is sensitive and responsive to forces far beyond its boundaries. That's a general sociological principle, and not surprising.
There is something interesting about this, however. For, as you may have heard, Godless Communism collapsed around 1990. And in recent years, that has changed a lot of things, including the rise in the acceptability of "socialism" in public discourse in America (and the rise of "Democratic Socialism"). Maybe the stigma against atheism will decline, now.
If so, it may be helped, in a complicated way, by two other factors that seem to militate against public approval of organized religion. Those are, respectively, the idea popular among Republicans that "radical Islam" is the US's major enemy in the world as a whole; and the perception among Democrats that domestic religion is nothing more than the false-consciousness of reactionary white conservatives to a changing America. (That sets up a false parallelism between those two things, but for now let it lie; I will say more about both of these facts in other posts.)
With people on the right opposing "radical religion" with the face of Osama Bin Laden, and people on the left opposing "radical religion" with the face of Franklin Graham, the public prospects for atheists and religious people may indeed flip in coming decades.