The atmosphere rotating at the same speed of the earth has very little to do with it.
Example: If there were no atmosphere and you jumped you would still fall in the same spot.
Its all about relativity. The plane, even at standstill is travelling at the earths rotational speed (1000mph). When the plane takes off there are two primary forces acting on the plane (in relation to this question), inertia, and gravity. Inertia keeps the plane at speed relative to the earths spinning speed. In regards to the question the atmosphere only really provides relative drag (outside of the whole aerodynamics side), ie if the atmosphere were not rotating relative to the earths spin speed upon liftoff the plane would either have a 1000mph tailwind or headwind.
So the answer is inertia, gravity, and very little to do with atmosphere.