The Atlantic magazine has an article in the May 3 2016 issue asking "Should Courts Get to Define Religion?"
The article deals with a Catholic shrine in Attleboro Massachusetts, Shrine of Our Lady of LaSalette, that covers almost 200 acres of land and includes what are undoubtedly religious places of worship as well as a coffee shop, conference rooms, bookstore and grounds that are decorated during the Christmas holidays with lights and Santa Claus and all the other gimmickry that draws thousands of tourists to see the Christmas display.
The state has a colonial-era law that exempts religious houses of worship and the dwellings of their ministers from payment of property taxes if they are used for religious worship or instruction. The town of Attleboro has in the past allowed the entire shrine property to claim the exemption, but on closer examination it concluded that much of the property is used for secular, commercial purposes and should be subject to property tax. The city sent a bill. The shrine paid but is seeking redress through the courts by arguing that the entire 199 acre compound is used for religious purposes. Not surprisingly, religious leaders across faiths have supported a brief claiming that local governments can't "presume to deem whether one use of a religious organization's property or another falls within the definition of 'religious worship'. That's a claim, in other words, that a religion can proclaim that whatever it wants is to be respect as "religious use" and any government must accede to that religion's view of itself, even if the activities are clearly commercial in nature and the same as what other enterprises do as part of their money-making ventures.
Here's the problem. As long as we single out religious institutions and properties for tax breaks, we have needlessly entangled the state in determining "what counts" as a religious institution or religious activity. I do not think the First Amendment was meant to, or should, protect religious institutions or religious properties from paying their fair share of taxes. I think the First Amendment was meant to protect a person's individual views from the particularized attention of the state, either positive or negative attention: that is, the State should not be able to target an individual for that person's beliefs. That is the core idea behind the notion of generally applicable laws: if public accommodations are supposed to be open to all, then no one can deny someone service based on either the owner's or the customer's religious beliefs. Religion should not be disadvantaged relative to other institutional organizations, but neither should religious institutions be advantaged. Accordingly, tax exemptions such as the property tax exemptions that exist in many U.S. cities and states, are problematic: they provide a special advantage to people who work in churches (tax-free housing for parsonages, etc.) and a special advantage to commercial enterprises run by churches (property tax exemptions for bookstores, cafes, flea markets, tourist venues, performances, and all the other trappings of religious institutions, made even more clearly egregious when the religious institution claims to follow a "prosperity gospel" approach that treats commercial market success as part of its religious activities).
The problem is that these tax breaks for religious institutions are in reality burdens on the religious freedom of all taxpayers who do not support that particular religious institution. They are impositions on taxpayers who are atheists or even of different religions from that religious institution, since any taxpayer is essentially subsidizing the tax breaks for those religious institutions that enjoy them. That is particularly problematic if most of the religious institutions receiving the break represent one main religion (such as Christianity, in the United States), whereas the subsidy comes from all of the members of minority religions or atheist households.
The climate in the U.S. today makes it even worse, in that almost any person can claim to found a religious institution, take in money to 'support' the institution, and live on the grounds of the 'institution' and thus enjoy an almost tax-free entrepreneurial religion-invention enterprise.
The solution is to get rid of all tax exemptions that favor religious institutions. Providing those tax breaks is not a matter of religious freedom--it is a matter of burdening the religious freedom of every person who does not agree with the supported institution.