I second Seely, you don't need padded bike shorts. I only wear bike shorts if I'm going over 25-30 miles or so. No problems riding the brooks in chinos or stand-up shorts for a 15 mile circuitous shopping menader or after work jaunt.

I think ride more, you'll get used to it. Is this the same bike you're riding from ten years ago? put on any weight, gotten sedentary in the last decade? Maybe a new bike, because biking shouldn't hurt (unless you're riding a brand new Brooks!)