If I were to guess (and bearing in mind I'm no expert, so they definitely are guesses), I'd say they are so expensive to rent for a multitude of reasons. Supply and demand is one; there aren't that many places that rent bikes, compared to the number of places that rent cars. Choices are fewer for the consumer, so demand is higher (for those that want to rent bikes, not for the overall population), and so are prices.
Bikes are expensive to maintain and repair, especially those big old Harleys. Those costs get passed on to the consumer.
Since you're 26 times more likely to be killed in a motorcycle accident than a car accident, this means that places that rent bikes have a much higher potential for civil liability than someplace that rents cars. Higher business insurance premiums translate to higher rental costs for the consumer.
I agree with you, it does kind of suck. There are places out west that rent bikes like V-Stroms, BMWs, and it would be nice to just fly out and ride, but for me the cost for a two week rental is just prohibitive.
"No matter where you go, there you are."