You are confusing states doing well with merely a few counties doing well.
http://www.citylab.com/politics/201...recovery-due-to-geographic-inequality/483989/
If your claim is that democratic control correlates to states doing well why are the democrats concentrating their benefits in only about 2% of the state they control? Is it that they don't care about the other 98% of the state? Or they can't figure out how to help people living in the other 98%?
If you look at counties with significant job growth the numbers tell a different story:
"D state": 31
"R state": 42
While there are more R counties the top 10 counties are evenly split between R and D states.
Obviously both R and D states can have this issue but to say that D states are doing well is to ignore a large swath of the state that is still doing worse than before the recession. I suspect that many of these feel left out of the recovery that passed them by and don't want a D president to continue the path of having the economy pass them by. (That doesn't mean that I think Trump will benefit them just that they likely saw Clinton as more of the same - which hand't benefited them at all). There are also cases like Michigan and Illinois where D control hasn't gone so well for them