The Falcons dominated the lines. Eagles couldn't run or protect McNabb. The Eagles may have miscalculated and let too many linemen go.
The loss of Trotter was a real blow to the Eagles defense, the Falcons were able to jump on them early, and the Eagles couldn't move the ball with any consitency.
It's early in the season, so the Eagles have a chance to deal with these flaws. IMO, McNabb is still the better QB, but without any time to operate he can't be effective.
Throughout their rise to the top the Eagles have been able to control the line of scrimmage on both sides of the ball. The teams that are able to contest with them there are the teams that can beat them. That includes the Steelers, Patriots and now apparently the Falcons.