Everything that has been posted so far about RockSim's estimates are true in my experience. But much of the discrepancy may be due to inexact estimates of mass, inaccurate finish settings (which are themselves rather general), imprecise or inaccurate launch site and conditions settings (this is also difficult to match with the exact conditions at the time of your launch, even if you knew all of them) and the presence of some design elements that may be difficult to model accurately (not as big of a problem as the others, but still a nagging one in a small number of designs).
With all of that being said, the estimates can often be surprisingly close when the program is given appropriate and accurate data to work with. My pre-flight simulations seemed to agree almost to the inch with my Javelin XL's flight for my Level 1 certification. I didn't have an altimeter on board to verify this, but it sure looked right and the time intervals and the landing data were all absolutely dead on. It was the maiden flight for that rocket, which I had only completed the night before and had only attached the rail buttons an hour beforehand, but it went exactly as I had expected. Not all of the sims nail the real thing this precisely, but time and time again they have been close enough for me to regard the program as an incredibly useful tool.