My guess would be that during launch and reentry the astronauts are wearing pressure suits that include a backpack, are custom fitted and probably provide padding. In orbit theres no need for padding on the seats.

http://en.wikipedia.org/wiki/Advanced_Crew_Escape_Suit

Yes, they wore ACES suits[1], which are partially pressurised.

Of course, at launch they wouldn't be sitting on the seats at all, they'd be lying on them.

[1]:http://en.wikipedia.org/wiki/Advanced_Crew_Escape_Suit

^ Too late for me to edit this, I should have said fully pressurised. The LES, the suit used on shuttle missions up to the late 90s, was partially pressurised.

I was talking to a stunt pilot recently, and asked him about that (the stunt plane on display had pretty much the same amount of padding). Apparently the padding (at least for them) compresses when you're under a high number of G's, and it causes you to move the joystick.

They're meant to hold people in space suits, not flimsy clothing.