A recent survey and report from Johns Hopkins' Center for Civil Society Studies found that, "Despite the belief that nonprofits are free of taxes, substantial proportions of [those surveyed] reported being subjected to one or another type of government tax or fee . . . ."
Typical fees included state or local government use or activity fees.
For example, a new Schenectady, New York fee will require all property owners (whether nonprofit or for-profit) to pay a "curb fee" based on how much of their property fronts the city's streets. This is supposed to help pay for road services.
In some cases, nonprofits are actually being asked to make voluntary payments in lieu of taxes. Why? To offset their use of government services.
I guess I'd feel better about governments requiring nonprofits to pay their "fair share" if it weren't that government is already shifting so much of the burden of providing services to an increasingly needy public right over to the nonprofit sector!