As has been pointed out already, the Bruins were devastated by injury over the course of the series, while the Flyers got key players back in their lineup at the same time.
Krejci going down in game 3 was the breaking point. Their centers were Bergeron, Savard -who shouldn't have been playing after the Cooke hit - Steve Begin, and Trent Whitfield. After Sturm went out, their wingers were basically Lucic, Recchi, Satan, and nothing else.
Just a shell of a lineup from games 4-7, if they survived, Montreal would've been favored in the ECF, and Chicago would've destroyed them in the SCF
I believe over the course of the comeback Philly got Carter and Gagne back as well.
They still should've won game 7 after going up 3-0 in the first period. I've always felt Rask is holding most of the guilt for giving up the softest goal I've ever seen in my life to get Philly back in the game right at the end of the first period. But the Bruins in general have more of an excuse for losing that series than the 2014 Sharks do for choking to LA. They always get off the hook for some reason while people mock the 2010 Bruins, who pretty solidly exorcised their demons the following season.