Of course, this is gratifying to my atheist ego, and that's the string they pluck on in the tiny article. It's also a strong theme in the comments: we've become atheists because we were smart enough to see the absurdity of religion. It's only the dumb sheep who stayed in their worn-out communities of superstition. Hell, Richard Dawkins has written books that do little but pluck on that string.
This is obviously not true. There is and always has been a large, networked community of religious intellectuals, and a large number of religious people in intellectual communities. The hypothesis that religion is something that happens to stupid people is so easily falsifiable that I'm embarrassed for all atheists whenever I hear it articulated.
And the actual survey also shows that the picture is, as you'd expect, more complicated than the NPR blurb:
Average number of questions answered correctly out of 32:
White Evangelical Protestant: 17.6
White Catholic: 16.0
White mainline Protestant: 15.8
No particular belief: 15.2
Black Protestant: 13.4
Hispanic Catholic: 11.6
Jews and Mormons are practically tied for first with atheists.
It seems to me that the biggest determinant is how easy it is to get into or stay in your group.
Most atheists have been raised in a religious family, and made a choice to break with that tradition. And even by the most inclusive definitions, at most 15% of Americans identify as non-religious (which in this survey would include the low scoring no-particular-beliefers). Mormons and Jews represent only about 1.7% and 1.4% of the population, and have traditionally, ah,...not been welcomed with open arms by the Protestant and Catholic majority. Becoming an atheist, Mormon, or Jew and staying that way in the United States will probably take more reading and consideration of sources than just being born a mainstream Christian and staying that way in a community overwhelmingly dominated by casual mainstream Christians.
I expect that if the survey could be controlled for effort expended on religious belief, the folks who came to Protestantism or Catholicism through a long and painful journey would score just as well as or better than the atheists.