The assumption of the statement, that taxation is the neutral starting point and tax-exemption therefore shows bias, is false. The default state of humanity is to be free from tax. All taxes are deliberately created by given societies. Thus to be free from tax is the neutral starting point and it is adding a tax which would show bias.
If not paying tax is the 'default' state of affairs, then so too must be not receiving the benefits of taxation. Yet the rule of law, state funded infrastructure of all kinds, protection of property etc are all tax payer funded benefits that enable and sustain church activity. Receiving and being advantaged by such taxpayer funded benefit, but having no obligation to pay tax, represents clear state favoritism towards churches, and thus entanglement of church and state.