Yep. To me, most faiths teach dogmas that are based in a notion of clearly identifying good and evil. For example, God v. Satan. Also, to me, most faiths teach dogmas that reach into the most private spheres of our lives. For example, premarital sex, birth control, homosexual thoughts, etc. And our First Amendment allows for this (as it should) provided nobody is ever forced to attend church. As such, it more than stands to reason that churches will reach into the political sphere as well. In other words, if a church is going to tell me when and with whom I can have sex, a church telling me to who to vote for (or not vote for), and even that one side of the political spectrum is "evil," seems inevitable. And it should be the right of the church to do such things, just like it is my right to publicly denounce such nonsense.
The government should be taxing churches and then leaving them alone entirely unless and until there is reasonable suspicion that a particular church is engaged in unawful and/or criminal activity.