Upvote:3
You can get data from http://flightaware.com about the time of recent commercial flights between two airports. For example, here is a list of flights from Denver to St. Louis. Each is shown with its scheduled arrival and departure times, but if you click on an individual flight, you can see the actual takeoff and landing times.
For airport pairs that don't currently have commercial nonstop service, I don't think you can do much except estimate based on distance.