Since taxes are not just for raising funds, but also for coercing/ encouraging certain behaviors, or even as penalties for not participating in certain behavior

Since taxes are not just for raising funds, but also for coercing/ encouraging certain behaviors, or even as penalties for not participating in certain behavior, then any tax on religious organizations is arguably the state imposing it's say on how the organization should/must operate. This is problematic on its own, but becomes worse if the tax laws don't result in equal treatment. For instance, a rule that exempted collections on Sunday from taxes, but not any other day results in favoring some religions, even if the rule is applied equally to all. And the extreme case is that the government could just tax all religious orgs out of business, leaving us with religious freedom, but not any churches to join.