cycocommute warned me last season about putting the hook over the fender. Apparently, the bus driver had to pull over for him to adjust it. I think it was in danger of falling off.
All bus instructions state to put it under the fender.
I run sks fenders on my touring bike. Everyday I use the bus and have no issues. I simply pull the fender up a little to allow the hook to cover the tire. Fender material is fairly flexible. My old freddy fenders were mounted on my hybrid slightly higher to allow the hook to engage.