I used to carry my shoes inside of an old pant leg that I had sewed closed at the bottom and put it in my pannier or backpack. Kept them safe from scuffs and dirt. I now just leave them at work.

http://www.ebay.com/itm/2-Plastic-Sh...item33704b3c3b

Something similar to this would be much lighter than the wood version. Haven't tried them though.