Whilst being a very good team they don't have that invincible aura that Barca had. Teams went into games knowing they had near enough no chance of winning. Strikers/midfielders knew they'd barely get a touch, defenders knew the only way to stop the constant flow of attacks was to foul and keepers spent the majority of the game picking the ball out of the net.
I think La Masia and the playing style is a factor as well. The majority of the starting XI came through La Masia and they were also the core of the all-conquering Spain team. Real are very good at adapting to suit the game/opposition. Barca played one way and were so good other teams had to adapt to them.