It's going to go against the grain at hackernews, but taxing churches in the US is a terrible idea. If you wanted to further the divide between the "liberal city"/"conservative rural" American cultures, this would be a great way to do it.
If you grew up in a rural area of the flyover states you would know that churches form the backbone of these rural communities. For example, the church in my hometown organizes youth gaming nights (yes, D&D style), widow support groups, and hosts food drives along with so many more things. They're so poor that every year they have a board meeting and the board divides up the operating expenses that are unpaid and they pay them out of pocket. The board members are 'well-to-do' community members with job titles like firemen and teacher. If they were not tax-exempt, they would have to shutter.
This is not to condone or justify the negative impacts that some churches have on this country, and religion often serves as a cloak for a lot of bad cultural habits like racism. I understand why people want to combat abuses of the non-profit status of the church, but taxing them is not the way to accomplish this.