My Pista feels really springy and absorbs a lot of bumps, but when I ride without my bike shorts I feel it a lot more.
I bought some very light padded elastic bike shorts from Nashbar that I can wear all day under either regular trousers or baggy shorts if I have to, and I forget I have them on.
The maker intended them as underwear.
Besides the padding, the elastic bike shorts just keep everything nice and tidy, and where it belongs.
Nuthin' gets pinched or squashed.
Usually, I wear big baggy shorts as outerwear, except in freezing weather and then I wear windproof bib tights and baggy shorts.