Just a word of caution in using the distances generated by the analysis I have proposed (and all of the other suggestions I have seen here). The distances reported would only really be true and accurate if there was no change in elevation due to either topography or flight ascent and descent. It is an accurate as-the-bird-flies distance only if the bird were capable of flying nearly at ground level and at a nearly constant elevation.
I would tend to assume that adjustments for altitude would support using the shorter distances, because I would assume that the altitude between destinations would not have to be as high in most short distance flights. However, the distances for take-off and landing or climbs and descents due to terrain and building obstructions would not be accounted for without some kind of elevation data for each point (and possibly elevation data for tall obstruction points that might intervene between your destinations, such as mountains, tall utility obstructions, high-rise buildings, or no-fly restrictions for military bases or other sensitive instalations). As long as those disclaimers and limitations are noted, the distances obtained from the analysis I proposed are reasonable as an estimate for as-the-bird-flies distances.