What kind of bunny is he? Is he a long haired type? These with longer fur tend to be more prone to matting-keeping the butt-fur trimmed can be a big help. Also, at least several times a week try to brush him. This should keep matting from happening so much.
If you're trimming out the matts, be VERY careful not to cut to close. If you trim to closely to the skin, its really REALLY easy to miss seeing skim in the matt and pretty quickly you have a bleeding bunny.