Any thing that exist as an organization with paid leader, be it a secular charity or a church organization should be taxed equally. Though it may be a well intentioned system to give tax breaks to religious and "non-profit" communities, I believe all exemptions to be misguided. One major problem is the line in the constitution that states "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof" We have tried to keep the intentions of non inference in tact while allowing/ mandating congress regulate our daily practice.
This occurs because in order to give special tax breaks one must put special stipulations in place. It is not special unless one define what ideals or actions do and don't qualify. This effectively puts any organizing registered as a non-profit under partial government control and regulation! Any attempt to enforce this could then be argued as an attack on religious freedom! The court is now forced to decided what does and does not qualify as a legitimate religious belief or institution thus putting it at odds with the constitutional mandate that it can not. The result is either yielding your religions definition over to the state and popular opinion or allowing just about anything and everyone to claim religion as a way out of all taxes. This situations is a conflict of interest for the courts and for law makers.
I understand that such a move may be difficult and the idea hard to swallow. Especially since many churches and organizations do a lot of good for the community. However it does little good to simply close the loophole applying to non-profits when many others exist that effect corporations and business in all sectors of life. What the church should be pushing for is common sense tax reform that closes loopholes for everyone, including the church. Such a tax code must be easy to understand and must not treat anyone differently regardless of income, race, position or beliefs. Anything short of this will continue to put minority views at risk and require daily compromises for anyone who wishes to hold these views and make a living.