It's the difference in the stand over clearance. You want 3-4 inches on a mountain bike and 1-2 inches on a road bike. The frame is measured from the center of the crank to the top of the seat tube. Since the top tube connects to the top of the seat tube it determines the stand over height. If you put your mountain bike and road bike side by side the seat will be close to the same height. The higher top tube on the road bike gives it more stiffness for better power transfer.