Yes , you fly with the spin of the earth, and with the spin of the atmosphere, and you reach your destination. That surprises you? Interesting. Does it also surprise you when you reach a destination when you drive a car that is moving with the spin of the earth?
Yes, there is no "barrier" between the vacuum of space and the atmosphere, there is also no friction. So there is literally nothing to slow the atmosphere down from matching the speed of the earth's rotation. And of course the plane is travelling 550 mph faster than the atmosphere, so a large amount of wind will result from the roof being torn off. The point was that you can be travelling at a good rate of speed, yet still being able to enjoy a drink. And when you are standing in your in your living room enjoying a drink, you are travelling at exactly the same speed as the atmosphere, just like the air inside the cabin of the airplane. So no 1000 mph wind, because the atmosphere is traveling at the same 1000 mph that you are, just like the air in the plane cabin is travelling along at the same 550 mph as the plane is.