Even though the Prius has been out a while it's still a bit of an unknown. You have most of the components of a regular car plus the hybrid components. Yes I know you have no starter, alternator, torque converter, etc. but you have a tremendous amount of new and different components as well as a tremendous number of "black boxes".

It's also a marketing thing. They can charge more because of the unknowns, even if it's just as reliable. Plus the unknowns get people nervous, so they'll be more willing to shell out the $$$.