I used to commute in jeans, but I traded them in for shorts made of coarse grit sandpaper to increase my comfort. I eventually worked my way through rough burlap before deciding on tight fitting lycra with a soft chamois.

Seriously, I can ride in jeans for a few miles, but for more than a few miles they really rub me the wrong way. I do, as other have mentioned, grant the world the courtesy of wearing loose shorts over the bike clothes.