This is a tricky one because churches are not for profit and taxing not for profit companies can hurt some companies.
I have issues with those super churches like you see in the picture I posted. I think if you have a billion dollar church and your funding is not transparent, then I think you should be taxed. That's only if you can't show how the money has benefitted the homeless, poor, etc... For example if your church is bringing in $500,000 a year and $300,000 is going towards building an extravagant church and for the minister, priest, pastor, or whatever to live in a $400,000 home. Then yes, those churches should be taxed.
The smaller churches, I would have to say don't tax them.