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They are given them because of the assumption that they are charities, regardless of whether they act like them.
"Churches (including integrated auxiliaries and conventions or associations of churches) that meet the requirements of section 501(c)(3) of the Internal Revenue Code are automatically considered tax exempt and are not required to apply for and obtain recognition of exempt status from the IRS. Donors are allowed to claim a charitable deduction for donations to a church that meets the section 501(c)(3) requirements even though the church has neither sought nor received IRS recognition that it is tax exempt. In addition, because churches and certain other religious organizations are not required to file an annual return or notice with the IRS, they are not subject to automatic revocation of exemption for failure to file. See Annual Return Filing Exceptions for a complete list of organizations that are not required to file."
https://www.irs.gov/charities-non-p...s-and-conventions-or-associations-of-churches
The "freedom of religion" argument is a red herring and I'll be ignoring it as a matter of course.
Its not a red herring its sole reason why churches are tax exempt, the reason people get to use the deductions is along the same line of reasoning.