A good pair of padded shorts really helps out. When I first started riding I had trouble withstanding just an hour of riding, now I can get up to 3-4 hours with only mild discomfort.
And yes, you often have to 'break in' your bum bones... you'll notice it getting better after a few weeks!
I'm starting a new career that can be physically trying. To get into shape for it I spent several months on a StairMaster and noticed that I really built up my butt muscles!!! I just purchased a new bike (have not ridden for quite some time) and in the last few days if I could have ridden 24 hours a day and even slept on the bike at the same time I would have! I was terrified of getting back on the bike today but I found that my butt does not hurt haha. I was surprised!
So if you have a gym membership I suggest building up the butt muscles before riding season and you'll be set! haha (Although, I maybe eating my words by tomorrow)