One of the key arguments offered by those who oppose tax exemptions for churches and religious organizations is that tax exemptions constitute a type of subsidy for these groups. Subsidies for religious organizations are unconstitutional, however, because they represent a means by which churches are able to obtain public, taxpayer support for their religious goals.

Its only among people of christian descent will you hear such questions. You will never hear a muslim raise such a question of mosques paying tax.
Infact, abusing the liberty we have in christ we so much question our faith,church,leaders,pastors that even muslims join us to do same while carefully leaving their religion out of it.

It depends greatly on their legal status. Most churches are recognized by law, in Nigeria, as not for profit organisations. This gives them the rare privilege of being exempted from CIT (Company Income Tax) and to a limited extent, some of their activities are also tax exempt, especially those 'economic activities' that are of a public nature.

The above notwithstanding, the government can still derive income through tax, by applying the tax instrument to the taxable income of the Church's employees, which also includes the taxable income of the pastor. In other words, church employees are not exempted from PAYE (Pay As You Earn) tax.

Churches are however required to pay tax when they engage in some other economic activities that are not of a public nature. This implies that ultimately, everyone is taxed (including Churches) one way or the other.