This current tempest is all very much brewing in a fucking Teapot. That Obama rushed to apologize about it to the whinehards, reminds me of that Breitbart scandal, when the Sec'y of Agriculture rushed to fire an innocent Dept. employee before realizing Breitbart had used her video clip out of context to stir up trouble and slander her.
I worked for a 501 (c) 4 citizen lobbying group back in the '90's. Donations to us were Not tax deductible, and we paid business income tax if we netted anything (usually not - was run as a non profit) because we lobbied politicians. It was an environmentalist group, rather banal and non-controversial....fighting toxic waste site building proposals and suing shitty law breaking landfill owners,and we got curbside recycling enacted in hundreds of towns and counties throughout Georgia. We were periodically reviewed or queried by both IRS and Georgia Dept of Revenue.
Since this particular IRS inquiry is new in format, I wonder if it is more than just consequent to the new allowances on donations, as stated in the article, but also because of the anti terror group/anti hate group funding laws. If your organization has those key words, which are coincidentally also used by known domestic terror, militia, and/or hate groups, yeah you're gonna get looked at.