if you just count flights that cross the state without takeoff or landing in the state, it's Virginia, then Maryland, North Carolina, and Pennsylvania.
Alternatively, you can look at the states with the highest ratio of (flights that cross the state) / (flights that start or end in the state). That's Delaware, which in 2014 had zero airline service. After Delaware, Wyoming, Alaska, Montana, Idaho, and the Dakotas.
Finally, coolest map today. For each state, which airport generated the most flyovers.

http://www.businessinsider.com/which-states-are-flown-over-the-most-2014-10