I am not sure, but I think that the tax-exempt status was granted to churches because they were seen as providing care and sustenance to the poor and infirm. In small communities, churches largely fulfilled this expectation for their congregation and to a lesser degree to the community in general, but often excluded those of a different color from their largess. Today, governments, municipal, state and federal, principally provide these services.
Individual churches, mosques, synagogues, temples and other recognized houses of religion should not be denied this status because the tenants of their faith that they practice discriminates. However, businesses should not have the same right. Morality, as defined by a religion, is to be embraced by the individual but not imposed on society. Everyone should have the right to choose a religion or reject them, but no one should be denied access to goods and services provided for profit because of their choice.
Taxes are necessary for governments to maintain and operate infrastructures that communities require. A flat rate, similar to the ten percent tithe many faiths request of their membership, would be reasonable if taxation was free from exemptions created to manipulate the actions of people, businesses and corporations, and the tax-exempt status for megachurches should be reconsidered. Exemptions should be allowed for not-for-profit organizations, especially those that do not pay the members of their boards of directors. However, it is unreasonable to tax the incomes of a significant proportion of our population that are insufficient to sustain them.