Some of the contributing causes to a painful butt are
1)maintaining pressure points for extended times
2)moisture
3)chafing
1) is the most common and can be somewhat controlled by choosing clothes that DON'T HAVE a seam across your butt. Get a seat, or ROJO, or sheepskin (my fav) that spread pressure out. Standard underwear and bluejeans are the worst in my opinion- they're always developing seams and ridges where I sit.
2) and 3) are closely related. If you get wet, the hair in your...sensitive areas...can feel like sandpaper. Again, a ROJO or sheepskin will allow ventilation. Pants that breath help out. Zip open the crotch area in your riding suit for a free blowjob Baby powder- or any talcum powder, really helps to absorb moisture and add some dry lubricant to the area. I just bought some "monkey butt powder" to test it out- it's talcum and calamine. Baby powder does ok for me, I'll see if this stuff is any better. FWIW, the folks at MCN seemed to like it.
Frequent stops to stretch help also, and like sports, long trips are something you just have to practice at to develop the stamina. Oh- and don't forget aspirin! That helps the joint pains.
I have a RM seat, a sheepskin and I wear trousers, rather than bluejeans on long rides. It definitely helps. The bicycle shorts are pretty nice also, but I only use them on 10+ hour days.