Don't know what others do but in the last couple of years I've taken to wearing over-the-calf socks while riding to keep my boot tops from chafing my legs. Wool ones in the winter (ski socks) and cotton ones in the spring/summer. Recently bought some of these to try them out and like them. They're so cheap I bought some more and now have twelve pair for <$10. If you sign up for the Sierra Trading Post Deal Flyer mailing list then you can get them for less then a buck/pair since they come in two packs.
http://www.sierratradingpost.com/p/10014,3436X_Terramar-Baseball-Socks-2-Pack-Cushioned-For-Men-and-Women.html
