Most of my friends who have roof racks either don't wash their car, don't use automatic car washes or end up taking their roof rack off first. I would probably recommend taking off the things like wheel holders, air deflectors, and anything else that could be considered even remotely loose. I don't think you have to take it all off. I have a Jeep with a roof rack although I don't have a bike roof-rack for it but the crossbars and such hold up fine through automatic car washes and I see no reason why the major components of quality roof racks shouldn't either.
Also, you can always give
this idea a try... no... not really.
