It is true that many churches do provide income, some of which is used for charitable acts and some for the advancement of the church's point of view, such as the direct or indirect support of political candidates and issues. The former should be considered exempt and the latter taxable. As individuals we file returns every year that separate taxable from non-taxable. This could easily be adapted to religious institutions and organizations in a fair manner.
It is very difficult if not impossible to differentiate what is a charitable act and what pursues a point a view. Many actions are a combination of both. If a church body helps clean up after a tornado, they have the opportunity to advance their point of view (beliefs) with those who have suffered from the tornado.