If this crew mistakenly tried to take off from a 3500 foot runway instead of the 7000 foot runway, then we need to understand why a competent and qualified crew made such an error. Short night of sleep, pre-dawn darkness, short taxi while blasting through the checklist... all possible factors. I heard (not confirmed!) that there was an AirTran pilot in the jumpseat... another potential distraction.
At some point during the t/o roll, options disappeared. Far too fast to abort the attempt without a high speed exit off the end of the runway, it would appear that a minimum airspeed rotation might have occurred. Unfortunately, as most of us can recall, they call that part of the power curve the "coffin corner"... raise the nose and you'll stall, lower the nose to gain airspeed and you'll settle into the terrain.
This accident, IF in fact caused by attempted t/o on a 3500 general aviation runway, will raise the issues of pilot fatigue and CRM to the forefront.