I think that it would be hard to charge a fee per item. Also might be a bad idea, because it could discourage people selling small stuff. I believe there are many members here selling small parts just to help others get their bikes on the road, and a per item, or per listing fee may make them feel like it's not worth it.
I personally have no problem with a fee. Another forum I belong to (not motorcycle related) requires a small yearly fee to list items for sale in classified section. The section can be viewed for free, everything else is free, but you cannot post a new sale thread unless. Just another idea.