This article is from the Model Rockets FAQ, by Wolfram von Kiparski with numerous contributions by others.
This is probably more for historical rather than technical
reasons. Since the motor is on top, a conventionally placed
rudder would be in the exhaust. In reality, some glider tails
are far enough from the exhaust that it often doesn't
matter. The real question should be "Why do airplanes have the
rudder on top?" :-) Aerodynamically, most would be better off
with bottom rudders, but that would get in the way of minor
things like wheels and the ground.