The average normal/heroic raider may know their rotation.. but they don't always know how to get 99% efficiency out of their class while being able to continually maintain high awareness.
If you don't see the difference being knowing your rotation and truly mastering a class (like every top 10 guild raider does), I just don't know what to say. There are different levels of class mastery.
The average high end guild probably has better communication, leadership, teamwork, synergy, etc than the average normal mode guild, but the also have players who are significantly better at the game.