This is all very uncritical.
What taxes are we talking about? Income taxes, property taxes or consumption taxes?
On income, congregations are, typcially, not-for-profit corporations and registered charities. Why should one kind of not-for-profit organization pay tax on it's operating surplus, while the rest do not? Religious organizations should be treated no differently than schools, libraries, community centres, museums and all the other non-profit organizations out there.
On consumption, religious organizations DO pay tax in most jurisdictions. If you pay for goods or services, then sales taxes are added on whether you are a private individual, a non-profit or a business corporation.
Only in the area of property do I see a disconnect. It should be patently clear that buildings owned by congregations but used for secular purposes (e.g. schools, hospitals, shelters and the like) do not qualify for a religious exemption from tax. Clergy residences are in a gray area, but typically would not qualify either (at least in this country). Purely religious structures, such as churches, mosques, synagogues and missions normally would. I really see no reason why this should be, but the actual impact on municipal revenue is likely negligible.
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--James