This video gives a pretty good idea of how the thing works:
Basically, there is no way in hell that one of the academies should be blowing any sort of major college football team out in a bowl game. Navy beat Notre Dame this year, narrowly missed beating Ohio State, and now this.
The wishbone did not die because anybody figured it out or it became outmoded; it died because the NFL viewed it as disruptive technology and athletes training for NFL careers wanted to be playing NFL-like football.
You still had to be able to throw the ball, otherwise opponents would just start lining up with ten or eleven guys on the line of scrimmage as the Fla. teams started doing against the Okies in the mid 80s. Alabama developed a sophisticated passing game integrated into the wishbone and the flexbone appears to be a further refinement of the concept.
Joe Gibbs said that systems don't win football games, athletes do. Sorry, Joe, but that's clearly wrong and this system appears to be worth some number of points per game, everything else being equal.
Basically, the academies don't have the problem of athletes worrying about NFL careers, and it's easy enough to see why major college teams do not relish playing the Naval Academy.
In fact, much of the violence content of NFL football arises from the manner in which it is played: zone pass defenses, one or two runners in a formation, and quarterbacks contributing little or nothing to running plays so that offenses are effectively outmanned 10 - 11 on running plays. The wishbone/flexbone eliminates most if not all of that. Even quarterbacks are safer since they're usually being hit by people closer to their own size and they see it coming. The one man who you could claim takes any more punishment than usual in that offense would be the fullback, and the rules allow substituting fullbacks.