Yeah..some of the bus drivers here get pretty antsy when they see somebody starting to put a bike on the rack during rush hour, let alone locking it to the rack. I don't know what the problem is because they are still loading passengers even after I have got the bike on the rack and locked it. However, I have to say that the majority of drivers are pretty good with cyclists.
I generally just put the lock through the frame and front wheel to deter thieves. When I get to my stop, I can lift it off the rack onto the sidewalk and unlock it there.
Justen