Yes, the midnight special is an express train out of prision. Those in the US who may not have actually seen a speeding train, won't remember that the central headlamp on the front of steam engines moved back and forth sweeping it's light in an arc back and forth across the tracks. When the tracks ran close to a building such as a warehouse or Texas' Sugar Land Penitentiary, the engine's search lamp might fall on the building during its swing. I think the legend at Sugar Land was that if the light chanced to fall on your cell window, you'd be the next one to ride the Midnight Special out of there.

I don't know if this legend was common across southern prisons or was unique to the Sugar Land Penitentiary, mentioned in the song.

      - Mark