That's the thing about Müller though, isn't it? Ronaldo is spectacular and everyone looks at him. So, the best way to counter a team with Ronaldo in it, since they pretty much all build a team around his glory, is to just counter Ronaldo. Germany has shown it with Portugal time and again, Bayern gave Real a good run for their money, too, simply by taking Ronaldo out of the game.
With Müller, however, it's not that simple. He's not spectacular, he always has other players around him that are more "shiny" and draw more attention than him. So, do you take Müller out of the game? Most people would think you're bonkers. And he's also outsmarting 90% of the defenders on the pitch in any given game, it's harder to keep Müller contained than Ronaldo. Ronaldo will start getting frustrated after 10 minutes of not getting one pass through to him, Müller will just adapt and wait somewhere else for a pass to reach him. That's his strength. He's not as fast as Bale, he's not as good a shot as Ronaldo or Kroos, he's not as good a dribbler as Messi or Neymar... but he's free or creates space for other players, he constantly puts defenders into a difficult spot with difficult decisions... guard the open space so Robben doesn't break through or run after Müller who is off again on one of his treks...
Ah, so he learned this football lark in a library/classroom as opposed to the streets and parks of Munich.