If the President was going to go after 501(c)(4)'s why would he not have made a push to shutdown the organizations that were spending all of the money? An even better question, why would the Republicans ignore treasury reports that this was going on? Why would the scandal hungry House Republicans sit on this story while at the same time flogging faux scandals like “Fast and Furious”. Generally you can trust people to act in their own interest, this is especially true for politicians.
I think everyone ignored this until now because they either didn't believe it, or didn't mind. In other words the IRS did this on their own, but no one cared.
No one likes the Tea Party. Yes, the GOP needs their votes and their excitement, but the GOP loses seats every time a Tea Party member opens their mouth. Without the Tea Party we'd almost certainly have a GOP controlled Senate. If conservative donors want to donate anonymously, then GOP groups want to make sure that those donations go to big groups that they can control. The GOP doesn't want independent grassroots Tea Party groups involved in anything other than donating and voting.
Look at how much dark money has moved through 501(c) status organizations. Liberals aren't going to rock the boat while conservative groups are being targeted, and conservatives aren't going to complain when grassroots Tea Party groups are being shut down.
Political Spending by 501(C) Organizations