I sometimes fret about my dirty shoes touching my clothing when I pack my suitcase. Typically, they are pretty clean when I leave for a trip, but sometimes get dirty during my stay. If I don’t have time to clean them, I usually put shoes in a plastic bag (like the ones I get at Wal-Mart), I place them dirty side in on the sides of the suitcase, or I just put them face down on top of everything.
However, if I’m at a hotel, I love grabbing one of the complimentary plastic shower caps and wrapping that around my shoes. Works great for me — but then again, I wear a size 8. My husband, on the other hand, wears a size 12 and just sticks to placing his in the bag sole side up or in one of the dozen or so neatly folded plastic bags he usually brings along [you can read more about that, HERE].