Actually there might be more thruth to this than you expected. I heard yesterday that the referee was the same who lead the WCh final 2014 against ARG. He was criticized by everybody in the world who isn't German for missing a foul in the match which would have given ARG a penalty.
Yesterday the referee went out of his way to look very carefully whenever there was a potential foul by a German player. And it was really a masterpiece to be 100% certain (that's the rule!) it was "hand" while standing with his back to the scene. His decision was correct from a formal standpoint. Schweinsteiger hit the ball with his hand and his head. You *can* give such a penalty. The FR players obviously didn't expect a penalty, if you watch their reactions.
In the end this scene decided the game. Generally speaking you don't want a referee decide the game.
The other aspect is that Germany, for the first time in ages, has a real attack problem. They could have played for another hour, I doubt they would have scored a goal. Without the penalty this would have meant another penalty shootout.
France played cleverly used their chances. It's one of these rare games in which the better team loses and it's not undeserved.