the 2 times I've rode the megabus, there's been no more than 15-20 people on the bus, and 2 of the 3 cargo spaces were completely empty. I'm sure the official prohibition of bikes is for those crazy cases when the bus is actually full.
2 questions though:
1) do you really just throw your bike in an empty cargo compartment, or do you partially disassemble it or something? I'd worry about mine sliding around and getting all beat up either way.
2) how the hell does the megabus make any money?!