Let every person be subject to the governing authorities. For there is no authority except from God, and those that exist have been instituted by God. Therefore whoever resists the authorities resists what God has appointed, and those who resist will incur judgment. For rulers are not a terror to good conduct, but to bad. Would you have no fear of the one who is in authority? Then do what is good, and you will receive his approval, for he is God's servant for your good. But if you do wrong, be afraid, for he does not bear the sword in vain. For he is the servant of God, an avenger who carries out God's wrath on the wrongdoer. Therefore one must be in subjection, not only to avoid God's wrath but also for the sake of conscience. For because of this you also pay taxes, for the authorities are ministers of God, attending to this very thing. Pay to all what is owed to them: taxes to whom taxes are owed, revenue to whom revenue is owed, respect to whom respect is owed, honor to whom honor is owed.Christians have never had any doubts about paying taxes as individuals. However, in the United States churches have been tax exempt. There are those who call for this situation to change. Many believe that eventually the federal government will take away tax exempt status from congregations who confess the biblical teaching that condemns homosexuality as being sinful and rejects same sex marriage.
(Romans 13:1-7 ESV)
Erik Stanley has written a very helpful piece that states why churches should be tax exempt. He lists several reasons, but the most important is the following:
But there is also a constitutional reason why churches are tax exempt. Our history is one of an unbroken practice of exempting churches from taxation. Churches were exempt from the very first time the tax code was passed at the federal level, and have remained exempt in every iteration of the tax code ever since. Every state in America also exempts churches from property taxes. When the U.S. Supreme Court decided a case regarding the property tax exemption of churches, called Walz v. Tax Commission, it stated that providing a tax exemption for churches was a less intrusive option under the Constitution than requiring churches to pay taxes.
That makes sense when you stop and think about it. As the Supreme Court said in a very early case, “The power to tax involves the power to control.” Taxation is, in essence, a very strong assertion of control by a sovereign over its subjects. Exempting churches is a way to ensure that the state cannot control churches.