There are a few reasons for what happened:
1 - If the airplanes returned to the gates, federal regulations would have prevented the pilot and flight crew from being able to fly for 12 hours or something. So the airline decided to keep waiting to see if a flight window opened up. Other airlines also did this, but for as long as Jet Blue.
2 - Because so many flights did not take off, Jet Blue's flight crews were "out of position" for their next flights. Jet Blue did not have the staff trained to properly locate and redirect flight crews. Other airlines (having more experience) have a larger and better trained ground crew to handle these situations.
3 - Most other airlines cancelled their flights well ahead of the storm, while Jet Blue attempted to keep their schedules. This is why you didn't this be more widespread to other airlines.
I think they tried to do the right thing to keep their passengers flying, but underestimated the impact of the storm, and over estimate their emergency capabilities.