The hue and cry that applications for nonprofit status from conservative political groups may have received extra scrutiny from the IRS is obscuring the real scandal: political groups masquerading as nonprofits to avoid having to disclose their donors. Here's an excerpt from a PRWatch.org story from February 2012:
501(c)(4) non-profits are limited in how much they can participate in electoral or partisan politics. According to the IRS, "political intervention" cannot be their "primary activity," which has been construed to mean that no more than half of their staff time or financial resources can be directed towards political endeavors (depending on how they report to the IRS).
The IRS rules on what constitutes "political intervention" are murky and rarely enforced, and groups like [Karl Rove's] GPS have been involved in a significant amount of activities that would reasonably be considered "political."