For those of us who came from the pc world, it is a trial to master the controller, but I remember that learning to use the mouse and keyboard was just as much of a trial, if not more. Fast forward to these modern times, and you should see the crazy things my 13 years younger brother is pulling off on the ps3 controller. He's working on things like jumping off of buildings in COD4 and doing a 360 in mid-air before he snipes someone without hardly zooming in. He's great with the mouse/keyboard combo, too, but the ps3 controller is no great hindrance to his playing.
I'm firmly in your camp as far as preferring mouse/keyboard, but I can see how the younger generation have no problem at all with the controller. PC gaming is sadly in danger of becoming extinct as a major force in the gaming industry.