Mobipocket.com isn't really a good comparison. They have a deal with the stores that license their format that they will not compete on price therefore their prices will always be higher than any other place you could buy a book. This is why Amazon uses a format that is only nominally different. Otherwise they would likely have to abide by this agreement. No more $9.99 new releases. Stores like Fictionwise are more realistic. Still, it's the publishers that have the most influence on price. If they charge the ebook sellers a high price, the only choice they have is to take a loss or pass that on to the customer.
As xianfox says, there are certain costs that must be borne regardless of format and some additional costs that come specifically with electronic format. I do think it's still a bit high considering you don't have to absorb the high return rate you have with paper distribution but I think many publishers are also trying to recoup the capital outlays they had in starting their ebook divisions. Many of them decided to start their own storefronts. I'm no expert but I don't think that's a good move for most publishers. I think it can work well for some genres like it has for Baens. I bet Harlequin's storefront gets good traffic. Publishers have brand recognition in these fields. Most mainstream fiction consumers don't know who publishes their favorite authors. They want to go to one bookstore, not hit five publishers trying to find the title they want. I can't imagine their e-commerce efforts pay for themselves. It's overhead they don't need.
An additional note about DRM: Not only would publishers save money by not paying to license proprietary formats, I think many consumers would regard the DRM-free, open format book as more valuable. Many people who are aware of DRM regard buying such files as not really buying at all. It's renting. You can't guarantee you'll be able to use it for as long as you like so it's hard to justify paying as much for it as you would a paper copy.