If the soft tissue between your legs is being rubbed raw, change your underwear to something synthetic without a seam that irritates your taint. If it's being compressed (which can take the lead out your pencil) you need a wider seat.

The only thing that should be hurting are the bones you sit on, and this goes away after a week or two. Any soft tissue pain, especially from being compressed (numbness is a sign this is happening) should be sorted quickly.