I'm surprised that the driver let you lock the bike to the rack. Reason being, if for some reason (like an accident), then the bike could do more damage if it's not allowed to be jettisoned instead of being dragged.

If you feel insecure about it, lock your bike to itself- immobilize either wheel. I've been toying with the idea of running my cable lock through the frame and rear wheel. Of course, I don't live in an area where I feel theft from the bus rack is very high, YMMV. And if you're really paranoid about theft, get a folder and bring it on the bus with you.