While I haven't used a bus bike rack myself, I have heard stories about damage and theft, but that was years ago.

If memory serves me correctly the damage was because of the arm used to secure the front wheel would sometimes mess up fenders and/or racks and certain wheel widths wouldn't fit. I'm not sure though if that problem is still prevalent or if the issues had been fixed.

I've heard that theft usually occurred when someone would just grab it while the bus was loading or unloading passengers and the driver wasn't paying attention or was unsure of who owned the bike. However these issues took place in major cities.