Overpitched,
Your puzzlement is understandable, except that you are automatically assuming that the intertial energy of the aircraft is somehow tied to the earth's surface. Not true, the velocity can be referenced to any coordinate system, as long as you are consistent.
A great read about this is from the mind that first developed the concept, and the mind that Newton relied on to guide him: Galelio.
What Galelio conceived of was "Inertial Reference Frames" that allowed him to understand the behavior of objects. He surmised, and we somehow forgot, that any reference frame that is not accelerating (ie the frame is at constant speed relative to another) is as acceptable. The wind/sky reference is quite acceptable.