Because most people don't have an adequate grasp of the theory, and it is impractical to go around shaking each person telling him the real reason.
I'm either not communicating my point effectively or not understanding yours. I understand that the reason you have to take the whole course isn't necessarily something that's easy to explain. Which is why I don't think it's common sense to take the whole course, doctors orders or not. "Common sense," for Americans and our culture of anti-intellectualism, dictates that we be skeptical of experts when they tell us something that doesn't make sense. Mom knows best, etc.
To the layperson it doesn't make sense to keep treating an illness after you've recovered from it. Maybe it makes "common" sense to trust your doctor but that's a debatable proposition.
But for the sake of argument that it is indeed common sense to not listen to your doctor, would you be willing to place a bet with me that you could with ease convince people like randman and faith to take the entire course of antibiotics for evolutionary reasons? I currently have 5 whole dollars in cash. How much do you have?
They'd just call it "adaptation" and accept the reasoning, so I'd say that's an easy bet.