There can be two reasons for this, it really does cost more to produce it, or the publisher is evil
In some cases, the print book was created prior to the advent of ebooks, and so it costs about as much to create the ebook master files as it does to create the master files for a new print edition. If the expected number of sales of the ebook is sufficiently less than even a hardback print run, then it's not profitable for the publisher unless they price it up at a trade paperback or hardback prices. Thanks to the tower of eBabel, there's usually at least 3-4 formats the publisher must prep, although if they have good software, that conversion shouldn't be that hard. Even so, as someone who is involved at Distributed Proofreaders, I can tell you that even for a simple novel for which you don't have the original electronic source documents, the amount of time it takes to create the master files (for example, scan the book, OCR it, proofread it, generate XML master) at minimum is probably about 8-10 hours. Even if you freelance this, it's probably going to take a couple thousand to do this. Since our publisher is afraid of copyright infringement, add in the cost of DRM, another couple thousand. Add in Author royalties, the rest of the publisher overhead including profit margin, and the ebook store's markup, it really does cost more than $9.99 to break even if you have projected sales of about 2,000 ebooks.
In other cases, the publisher created an electronic master document from which the hardbound and mass market paperback editions as well as ebook formats are created. The publisher made the ebook available at the same time as the HB, and priced it the same as the HB. Then, when the MMPB came out a year later, the publisher kept the price of the ebook at the HB price. Why? Because the publishers don't like ebooks, they're afraid that ebook sales will cannibalize the print editions, and any cheap prices on ebooks will get the consumer to expect all books to be priced cheaply. You're proof of it, in their eyes.
In MacMillan's PR campaign for their side of the Amazon dispute, they claim that with their agent model, they will release the ebooks at the same time as the initial HB release, price it around the price of a trade paperback, and eventually drop the price to below that of a MMPB, presumably when the MMPB is released. This sounds good until you take a look at MacMillan's track record. Most of their ebooks are currently priced at HB or TPB prices, even though there's a MMPB available, and their TOR/Forge SF/F imprint has almost no ebooks available. If they really do change their ways, great, if not, it won't be any different from now, where I don't buy ebooks from MacMillan because either they're too expensive, or unavailable.