Its all in the sprocket gearing. If you have the same gearing running to the wheel for two different sizes of wheels, the smaller wheel will go slower than the bigger wheel.
If you think about the wheel size, it really determines the total distance that the wheel travels for one revolution. That old formula 2*pi*r gives you the circumference of a circle from its radius measurement. A bigger wheel will have a larger circumference, and therefore will travel farther for each revolution. Because of this the larger wheel will travel faster, given the same RPM as a smaller wheel.
You can alter the gearing to allow a small wheel to travel faster, which is why those scooters can go so fast with a small wheel.