You'll also have to deal with the critical speed of the shaft. You've basically just removed one of the big advantages of rack and pinion over screws - higher speed capability without having to worry about screw resonance. To get around that you could make the shaft a hollow tube, but that's possibly adding weight and size and is definitely increasing the inertia of the drive system meaning it takes more torque to accelerate at a given rate which leaves less force left to cut with.
Another downside is you can't support the bed anywhere between the ends as the shaft would have to travel with the gantry, at least if you put it under the table. A better solution might be to put it across the gantry. Then you could support it with bearings at shorter intervals to avoid some of what I talked about above. However I'd recommend you don't do any of this and just put a motor on each side. It works fine.
CNC mill build thread: http://www.cnczone.com/forums/vertical_mill_lathe_project_log/110305-gantry_mill.html