I would hope not, considering that I don't go around telling those friends of mine that happen to be Christian to go out and become active in politics.
Yes, religion has certainly been an extremely large, if not the largest, force in the history of mankind. It's also more involved in the State than some of us are comfortable with (see: Ted Haggard visiting the White House via telephone on a weekly basis during the Bush II years). However, I cannot see a good reason to tax religious establishments given the direction that this country (and the world) is moving in, religion-wise. The percentage of people in the United States who do not state a religious preference (the "nones") has increased from 8.2% in 1990 to 15% in 2008. In many European countries, "nones" are the majority. Meanwhile, the percentage of people in the United States who identify as Christian (of any type) decreased from 86% in 1990 to 76% in 2008. Given that the "nones" could be the largest "religious" group in the United States (or at least a very close second) in the near future, if you start taxing churches now, it could pose problems for religious freedom down the road. Given the constitutional guarantee of not prohibiting anyone's free exercise of religion, you can see how this could be a bit of an issue.
(Stats come from the American Religious Identification Survey, 2008)