The biggest losses are from changing rotation direction, and a shaft-drive bicycle does so twice (once from transverse to longitudinal, then once again to transverse).

Most shaft-drive vehicles use one or even zero power transfer direction changes - most RWD vehicles (both motorcycles and cars) with shaft drive have longitudinal engine rotation (although a few motorcycles run transverse, and a few RWD cars are set up like front wheel drive cars in the rear), only requiring one change of direction at the rear differential, and most FWD cars have transverse rotation, and use a gear or occasionally chain drive to send the power back a foot or so (maintaining transverse rotation), then keep it transverse to the rear wheels (but some (I'm looking at you, Subaru and Audi) have longitudinal rotation, send it back, then turn it 180 degrees, then turn it 90 degrees, which is horrendously inefficient, but lends itself to a simple all wheel drive drivetrain).

You'll also notice that engine camshafts are universally driven by either a belt, chain, or geartrain, all of which preserve direction of rotation.