(note that I'm talking about pc flight sims in general here)
I have never flown a real plane, but I'd assume that even if a sim doesn't teach you how to truly fly, flying in it could make you faster at learning how to use the real thing. Things are always easier to learn and understand if you have seen or tried them before.
Another reason why virtual pilots would likely have problems flying a real plane is that they tend to self study. If nothing else, it can easily lead into bad habits that seem to work but can actually be dangerous. I'm quite certain that if a real pilot would first teach you how to fly using the simulator, you'd then be much better off learning how to use the real plane.
So yah, simulators and real world have their differences. At least when it comes to pc driving simulators, I find that doing either one can help doing the other one, but it doesn't (necessarily) alone make you good or even average at the other. For example, a real driver have much more at stake and more things to consider, but then again he can physically feel the movement of the car, which is a very important thing. A virtual driver lacks this ability. This means that a virtual driver does not learn how to use this feeling and a real driver will suffer from the lack of it when driving in a sim.
Anyway, what is a fact for both simulator flying and real flying, is that doing them increases your field of percetion and makes you better at multi tasking. This should be an useful ability for both virtual and real pilots, and maybe even help you drive more safely :P