In the case of learning to fly an RC helicopter, this relates to the ultra fine control of our thumbs &/or forefingers, and thus we need to use the exact same controls we would in real life if we want to learn these necessary 'subconscious' skills. You know, learning something to the point you don't even have to think about what you are doing in order to do it, like walking or riding a bicycle. This is known as subconscious memory, or muscle memory. The main reason for this is anytime we are learning a new task, we need to build new pathways in our brains to control our motor functions. The only way to learn to fly with an RC helicopter simulator is by using a real (or at least gutted out) RC transmitter/radio.
RC Flight Simulator 'Real' Control Interface