Well I think that a flight sim is just like any other tool, used properly it works great and achieves the desired result, used improperly and it does not achieve it...
I personally found that spending a number of hours on the sim really helped when I got to the actually flying the trainer stage with my instructor/buddy. I did find that using the sim after those first few trainer flights created a problem in that it was too easy to push the reset button on crashing. So I quit using it for a period of time. Now that I've flown quite a bit more and want to try the IMAC thing, the sim is providing real good practice for new maneuvers using an imported copy of the model I fly with the physics/parameters modified for a more realistic performance. I also try to fly the sim just like a real model now in that a successful flight includes all phases, takeoff, maneuvers, and a successful landing. Adding in wind and other variables will also help improve your skill, or lessen the time required to attain that skill on a real model. All of the people/instructor types I've spoken to about using sims have said the same thing about them; that they are a real help in learning to fly and substantially reduce the cost factor of learning to fly.
It's really helped with trying to learn how to fly the micro helicopter I just bought as well...
So yes, a sim does have it's limitations, but used appropriately I think it is an invaluable tool for learning and helping to maintain eye/fingers coordination in between trips to the modelport, and a lot of fun when it's impractical to be flying the real model.
Just my opinion... [8D]