In general, land that you only see out of the airplane window.
Specifically, in the USA, pretty much anywhere that isn't either (a) a major metropolitan area or (b) a hot vacation spot. Especially refers to the Midwest.
flyover country carries with it a strong connotation of condescension; ie the only purpose Nebraska serves is to inconvenience yuppies on their way cross country. Thus it is rude to use the term in front of anyone who makes their home in flyover country.
Another salvo in the war between urban culture and rural culture, country folk vs city folk.