Pretty easy really. If a guy doesn't have the physical ability to play in the NFL it will show in the draft. For instance if a cb looks good in college but runs a 4.8 forty it's unlikely he will ever hack it at the NFL level. Or if a QB can only throw the ball in the low 40 mph he isnt going to be able to play in that league regardless of what else he does well. Mason Rudolph fell on draft boards because his arm strength was below average. Watching him play in college he didn't appear to have a issue with arm strength. But watch him in the NFL and it's obvious he has a major weakness in that area.
To me the combine is more to see if a guy who looks the part really has the ability. I hate it when teams draft a combine warrior, guy who wasn't very good in college but runs like a deer and lifts Volvo's