Answer:Because, first, the atmosphere is moving with the Earth’s Surface. Secondly, although you might aim straight up, you, the stone and the Earth’s surface are moving at up to about 1000mph depending on how close to the equator you are. So you throw the stone upwards at a few metres per second, but it also has the same horizontal momentum as you and the Earth’s surface, up to 400m/sec. So if you threw it up exactly vertical, it will come down nearly on top of you, unless there is a local wind blowing, in which case it might miss by a few feet.
Try throwing a stone sideways from a moving car. Aim at a tree you are passing. The stone will land a long way from the tree somewhere near 90° from your car. Because you have imparted two vectors of motion to it. One sideways from your throw, and one forwards equal to the speed of the car.