Regardless of whether you buy Yglesias's logic, this raises an interesting question — exactly how much money are we talking about here? If, all of a sudden, churches, synagogues, mosques and the like lost their tax privileges, how much tax revenue would that generate?
Ryan T. Cragun, a sociologist at the University of Tampa, and two of his students, Stephanie Yeager and Desmond Vega, took it upon themselves to figure it out. They're not exactly disinterested parties; their research appeared in Free Inquiry, a publication of the Council for Secular Humanism. But Cragun is a serious sociologist of religion and the data seems to check out. The full scale of subsidies religions get is pretty staggering:
When people donate to religious groups, it's tax-deductible. Churches don't pay property taxes on their land or buildings. When they buy stuff, they don't pay sales taxes. When they sell stuff at a profit, they don't pay capital gains tax. If they spend less than they take in, they don't pay corporate income taxes. Priests, ministers, rabbis and the like get "parsonage exemptions" that let them deduct mortgage payments, rent and other living expenses when they're doing their income taxes. They also are the only group allowed to opt out of Social Security taxes (and benefits).
Cragun et al estimate the total subsidy at $71 billion. That's almost certainly a lowball, as they didn't estimate the cost of a number of subsidies, like local income and property tax exemptions, the sales tax exemption, and — most importantly — the charitable deduction for religious given. Their estimate that religious groups own $600 billion in property is also probably low, since it leaves out property besides actual churches, mosques, etc.
Of course, these subsidies do more than reduce revenue. Property tax exemptions, in particular, distort real estate construction decisions and allocate more land to religious entities than would otherwise be the case, which drives up rents for everyone else (especially since religious groups tend not to buy property in high-density, skyscraper-style developments and instead get a whole lot of land for themselves).