Sure, but that is a political decision. There is no Constitutional ban on taxing churches like any other similar entity.
The government cannot treat religious entities worse than secular entities, but that does not mean that government is required to treat them any better.
Generally, it has been accepted that the First Amendment protected Churches against taxation by the federal government. The 501(c)(3) appeared to be a codification of this long accepted principle, but was actually a trick give Congress the authority to regulate Churches. For almost 200 years Churches enjoyed tax-exempt status with no strings attached. Now that magically comes with strings attached. Even now Churches are still 'tax-exempt' but only if they bow down to the regulations of Congress which is prohibited from regulating them.