IMHO, "organized religion" has been in trouble for quite some time in America, but it's had little to do with the economy. Molestation scandals in the Catholic church, sexual and financial scandals in various other churches, and a lot of people just not seeing the power of God at work in and through the 'people of God' at many churches have done no favors and given little positive press for organized religion in this country. Add to that what some could see as a lack of social justice or an ignoring of social issues by the church and then the over-politicizing (left or right) of other churches and many people have just formed a sour attitude towards religion, church and, worst of all, Christ.
The linked story seems to support this.
That said, I'm not going to brag on my church, but I will boast about how good God is as we've been one of those churches that has seen growth throughout the recession and I think it's for the simple fact that we preach Christ and Him crucified at the core of every message and Jesus and salvation in Him is the reason behind every mission and ministry. We're one of those non-denominational Christian churches that don't have to do what we do according to some regional district or convention. The Bible is our authority and Christ is our head.
I think people want to see that kind of definition in a church, instead of some of the wishy-washyness and flat-out anti-biblical stuff that's been going on in churches for years.
And while I have seen a couple local churches close up shop (for a variety of reasons) and others experience big declines in attendance/membership, I've also seen others grow and a few newer church plants begin and see initial success, so there's good news amidst the bad. Maybe it's just more "separate the wheat from the chaff" time going on...