One of my Brooks saddles is black (I have 3). Never had an issue with the dye, and I don't generally wear "cycling clothes." Brooks are made with very high quality leather, more of an issue is when I've put too thick a layer of Proofhide on and *that* has left a bit of a grease mark on my pants. (it has washed out)

When you put on Proofhide, rub it in well and buff it well.