IMO, there's no difference between the markup that a motorcycle dealer charges versus the markup that car/truck dealers charge. Take a look at your local car dealer's "certified" used cars and compare those prices to comparable private party sales.....there's a huge difference.....sometimes as much as 50%.
I live in NJ where the riding season is relatively short. Generally speaking, motorcycle dealers only have about 6-7 months of the year to sell their new and used inventory. As such, they need to make as much money as possible (within reason) to keep their dealerships alive during the lean months of the year. I'm not justifying how much more they charge than private parties, but they do incur substantial overhead to keep their dealerships afloat during the non-riding season and have to reflect that in their pricing. It's not easy being an independent motorcycle dealership.