I'm thinking about my taxes, which explains this erratic and perhaps erroneous line of thinking. PeaceBang's adds fodder to my thoughts.
First, churches are tax-advantaged in two ways: their property and income are usually not subject to tax, and their members get a tax deducation for funding them.
OK, I get the first as a state non-interference matter (more about it in a moment) but what about the later? Charities are tax advantaged because they provide a good to society that (unlike a mutual aid society) does not individually benefit its members. But a whole buncha churches provide only the most nebulous public good -- particularly if you factor out the debatable social merit of public worship, which I would expect the state to be neutral towards. These really do serve their members, and only society to a marginal, even ephemeral degree. Why should the members get a tax-deduction for this? I'm quite serious.
Or, concerning property taxation, why should a inwardly-focussed (essentially, antisocial) church be exempt?