I have no idea, but if I were trying to answer the question I wouldn't ask USA Today. This article by Brad Heath is really one of the silier pieces of journalism I've read recently. The headline -- "Billions in aid go to areas that backed Obama in '08" -- certainly suggests political manipulation. But that headline could just as easily read, I dunno,
"Billions in aid go to areas that backed McCain in '08"
"Billions in aid go to wealthy Americans"
"Billions in aid go to white Americans"
or pretty much anything. You'd have just as much tantalizing suggestiveness, and just as little factual content.
And about that factual content: The Heath piece basically says (1) counties that voted for Obama get more money than counties that voted for McCain; (2) pretty much all of this money "has followed a well-worn path ... guided by formulas that have been in place for decades and leave little room for manipulation." There is no theory presented for how the spending could have been manipulated.
The article concludes by noting that "From 2005 through 2007, the counties that later voted for Obama collected about 50% more government aid than those that supported McCain, according to spending reports from the U.S. Census Bureau." Yikes! Either that completely destroys the premise of the article, or this pro-Obama conspiracy runs far deeper than even USA Today can imagine...