hey - just contributing my 2 cents. When I commute to/from work, I turn the shorts inside out and wipe down the chamois with a clean baby wipe, and then let dry - hung up all day. It probably doesn't do much as far as bacteria is concerned (that stuff probably goes deeper than the surface) but I think it just gives me peace of mind.
Baby wipes are such a wonderful invention. After a long ride, when I have sweat a lot, having baby wipes in the car to wipe the scratchy salt off my face is sooo refreshing. And they're much cheaper than the Olay, or Ponds, etc facial cleansing wipes. I always figure that with the regulations being pretty strict with baby products, pretty much anything that says "baby" on it will be pretty gentle or soothing.
Good for you for commuting!!