Then again, maybe you missed THIS:
Sometimes circumstance plays a part in a player's career. The 49ers were so successful when Young first arrived they weren't about to start him over Joe even if he might have been better. Why mess with the chemistry? In later seasons it was clear the guy on the bench (Young) was better than the guy on the field (Montana). And by all accounts Montana was still pretty freaking good at that time.
Joe did not yield gracefully, unfortunately, and was a bit of a whiner when he was replaced. Still, after some time passed, he was wise enough to recognize that Young was the more skilled QB, as you can see from the quote above.
EDIT: One more thing (and I know you will just love this, Rico) Peyton Manning belongs on that list. No question.