Four main components to worry about
:
- Saddle
- Seatpost
- Shorts
- Your own butt
A couple of these should be obvious: get a comfortable saddle, padded chamois make a difference. A good vibration-damping seatpost is an often-overlooked part.
Your own butt can be conditioned to get more comfortable on the saddle, and the only good way to do that is ride a lot. There are going to be growing pains, but it'll get better. Also, move around a little during a long ride: change hand positions, sit up or lean forward, etc.
The geometry of your frame also plays a role, since it affects the position in which you sit. But it's hard to dramatically change that without getting a whole new bike. The only "easy" fixes here would be to use different handlebars or stem, and the fit of your bike might not be the problem in the first place. You probably don't want to screw around with the fit of an otherwise well-fitting bike only because your butt's sore. Try the other solutions first (unless you already thought the fit was off).