Most commercial flights are actually in the troposphere, which is about 17km deep in the temperate zone. Your point is still right: air density at 36000ft is ~0.37 kg/m^3, as opposed to 1.23 kg/m^3 at sea level.
To build on this, the drag force varies linearly with fluid density and quadraticly with velocity, so the four-fold increase in fluid density from airplane altitude to sea level corresponds to a doubling in velocity. Which is actually the difference we see! Cool!