other, necessary investigations.
This actually isn't the first noteworthy time that the IRS has investigated non-profits over the potential for abuse. There have been long-standing issues regarding the clarity with which federal tax laws regarding exempt status and political activity are understood, and this more usually makes the news in relation to church/state issues. For example, All Saints Episcopal Church was investigated regarding a 2004 sermon that may have criticized President Bush too particularly, and The United Church of Christ was investigated for its apparent support of 2008 Presidential candidate, Barack Obama. But other non-profit groups have also faced tight scrutiny, such as the NAACP, which was also investigated in 2004 aparently for criticism of President Bush. One could argue that the investigation smacks of having a partisan bias, but then again, the problem with separating raising political awareness, championing certain causes, and voter education with outright politicking is just that--an issue of partisanship.
Also, in the period just after President Obama took office, it should be pointed out that there was a swelling trend of new Tea Party and Patriot-named organizations being created. So I don't find it out of the realm of possibility that the agency was, in part, responding to a changing pattern in tax-exempt registration that bore looking into, without any particular direction to do so from above.
But that's just my quick take.