This piece is saying what some of us have been saying for a few years, and what responsible scholars (like Hout and Fischer, whom she mentions in her piece and I do in mine) have been suggesting for a lot longer than that.  Short story: the "religious right" has driven "liberals" away from religious institutions, and this is more pronounced the younger the cohort is (something the A T-D piece doesn't quite bring to the forefront as I think needs to be).  Political polarization in America has infected American religion in a powerful way.

Here's my theory of the case: the rise of the "religious right" in the 1970s and 1980s was itself (in part) a reaction against the large and inescapably religious movement around racial equity of the 1950s and 60s (which also expanded to larger issues of gender and sexual equity as well, by the early 1970s, as David Hollinger and others have noted).  But it produced a tighter association of religiosity and political identity among its members--much tighter than had been the case previously.  

In response, the liberal and progressive churches and religious movements had spent a fair amount of their energy kenotically, creating interreligious and pluralistic institutions to host the moral campaigns they had initially hosted and fuelled.  (Again, Hollinger is really good on this, at least I think so.)  So the response to the religious right was not a "religious left," but rather a (disorganized) liberalism in general.  (There is a larger story to tell here about the confidence of the right and the uncertainty of the left since the 1970s, but leave that to the side for now.)  

Then, something unprecedented happened: the Communist bloc collapsed.  The great enemy of Americanism, "godless Communism," had disappeared.  The fusion of religiosity and Americanism that became prominent in the 1950s (when "under God" was added to the pledge, and "in God we trust" added to the money) had nowhere to go.  Younger people had begun to associate "religion" with right-wing politics in the 1980s, and (perhaps because they largely didn't like right-wing politics), there was a measurable generational decline in religious affiliation in the 80s.  The 90s were a liminal time in this regard, with no major changes but the decline of religious affiliation among younger Americans continued.

Then, another unprecedented thing happened: 9/11.  Suddenly, America was challenged by a new enemy.  But this one was all too godly, though obviously not "godly" in the way that Jerry Fallwell and his friends meant.  (This, by the way, could be behind the attack on Islam as "not a religion" in the past decade.)  Still, the connection between a radical form of religion and perceived attacks on the "American way of life" didn't help.  And younger people continued to drift away from religious institutions.

As an aside, it's useful to note, as T-D does, that many people who are not affiliated with a religious institution still say they believe in a god, and a good number still call themselves religious, and many call themselves "spiritual but not religious."  There's not a lot of atheists in America, or even agnostics.  But the problem is that these people recoil from the institutions that have traditionally hosted, cultivated and sustained these sensibilities, and embedded them in larger civic patterns, have become for many younger people--and by now that means anyone under 50--pretty toxic. 

This is problematic for American civil society in lots of ways.  (One day I'll write a piece on the wonderful idea of "weak ties" for you all.)  But here I just want to note that it's hugely difficult for religious institutions themselves.  Presumably there are many religious leaders out there who want to care for their congregations, whatever their immediate political views.  (And I'm not saying that political views can't have religious implications--they obviously can--but I am trying to resist an identity between them.)  Insofar as religious institutions have a wider and deeper "horizon" of concern about their members than their members' politics, this presents a major problem for such institutions.  Or so I suspect.

Again, tl;dr: It's not just a civil society problem; it's a huge problem for religion in the United States.  And there doesn't seem to be any evidence that things are getting better.