Challenging Tax Exempt Status of Nonprofits

On the front page (well, front web page) of today's New York Times, there's an interesting article (here) reporting on a Minnesota Supreme Court decision that "said a small nonprofit day care agency here had to pay property taxes because, in essence, it gave nothing away." 

While it's clear that charitable organizations play a valuable role in our society, it seems to me that the concept has been taken a little too far. 

Nationwide, there are more than 1.4 million charitable and nonprofit entities registered with the IRS, accounting for 5.2% of GDP and 8.3% of wages and salaries.  Private foundations and other nonprofit organizations command $1.1 trillion in assets and reported more than $300 billion in revenue last year.  In short, a substantial and growing segment of the economy is not supporting the tax burden. 

I'm not saying we should do away with tax exempt status for all nonprofits.  But I do think that it's time to question what reasonably qualifies for this status.  Small day care agencies, like the one in Minnesota?  Rich foundations?  Universities with multi-billion dollar endowments?  Mega-churches with commercial and media businesses?  Are these entities so different from the rest of society that they shouldn't have to contribute to the tax burden?