Atletico more than deserve to win the match. Real simply pay the price for not respecting their opponent enough. Real started with the formation 4-3-3, an astounding decision by Carlo Ancelotti. They went to Vicente Calderon without Ramos, Marcelo,James, and Carlo still insisted on playing with 3 forwards.
Really Atletico had a hell of an easy match. With Arda Turan and Koke (and later Saul) played as defensive wingers, they had no problem blocking all passes from Real. It was impossible for Real Madrid midfielders to do anything else than to lose the ball time and again. They only have 3 players in the midfield: Isco, Kroos and Khedira. Even worse, none of them is a ball-winning midfielder. If Real want to play 4-3-3 badly, they need a physical figure in the middle of the pitch, such as Paul Pogba.
I hope Real Madrid players will consider this a lesson. They must play against Atletico and any tricky team with a more balance shape.