They should estimate the average stay length of their guests and amortize the cleaning fee appropriately, the same way that many other businesses (including real B&Bs, in my experience) handle fixed costs. In theory, AirBnb should be very good at automating the process (they have large amounts of very granular, market specific, historical rental data), but honestly, if that amount of planning and bookkeeping is too much for the rental operator, maybe running a B&B is not the best career fit for them.
It's fairly routine for B&Bs to have a 2-night minimum on weekends but, yes, they typically also just have a nightly charge (which may vary depending on day of week) and don't have a fixed per-stay adder.
AirBnBs have definitely normalized a significant per-stay charge that isn't the norm in the hotel/inn business.
