It's not. At least not in the current state of things. Many churches were built on vast chunks of land long ago when real estate wasn't what it is now. The government is missing out on oodles of property tax they could be putting to use but can't touch.
If it were up to me, the government should be able to buy back chunks of unused property (all those giant lawns...) to be repurposed for other things. Churches and other abrahamic religion-based institutions shouldn't mind too much. Their religions do preach modesty after all. And if that property tax money is going back into the community, who can complain really?
If we're talking about out in the country where land is a-plenty, then who cares. Those communities don't require as much maintenence or public services anyway.
Of course, this means reasonable taxation. A lot of churches barely make enough off collection to get by, and taxation should by no means tighten a financial noose around their necks. There should be SOME standard for it though. Exemption is a bit much. There are other churches out there that can afford backlit rooms, comfy movie theater seating, and brand new mega TVs in their mass halls. Those guys don't need exemption to survive.
The Church of Scientology should just straight up pay all the taxes on everything they do. Same for "Churches of Christian Science." If they're going to claim they are first and foremost "scientific" they are forfeiting the title of religious in favor of something else entirely, no matter how faith-based it may be. It's no longer a religion when they take that step, I think.
PS Maybe change your wording, since this subject would also include mosques, synagogues, and any other property owned by a religious institution.