I don't have an answer for you, but I've wondered the same thing as regards my car bike rack (an earlier version of this one:
http://www.thuleracks.com/thule/imag.../thumb/916.jpg). It holds the front wheel in a similar manner to the bus racks I've seen, and I've wondered about possible damage to the fender -- or if I could engage the hook just in front of the fender and still achieve a secure grip on the wheel.