It does make sense for them to be more expensive, as it takes more time to develop cross device apps (to do it properly).
You have to develop a different viewport for each one, and doing it properly will require a different UI..which is arguably one of the most time consuming aspects of iOS development.
I've only been learning so far and creating iPhone 4 apps but I would definitely be charging more for the iPad versions if I ever get around to releasing anything, due to the extra development, testing etc that goes in to it.
I guess that another reason is the different markets that the iphone and ipad go for - I suspect that the demographic is different for both (I know many more older people with ipads than iPhones), so the “sweet spot” for pricing is higher? No evidence for that last point tho, just an assumption :)