The Eagles lost the Superbowl because they were the poorer team. The game didn't seem as close as the 24-21 score would indicate. McNabb did not look very good, missing many of his passes badly. Even decision-making at the end of the game (an onside kick that gave the Patriots excellent field position, and attempting to complete passes in the middle fo the field with 30 seconds left and no timeouts) implied that the coaching staff was not up to the challenge.
The Eagles had the best season of their existence, but they still came up short of giving the city of Philadelphia, and their fans, the championship they have been craving.