An article on Cnet News, "Publishers want more to publish on iPad":
http://news.cnet.com/8301-13579_3-10454230-37.html
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Essentially, what it comes down to is control. The Financial Times says that "ownership of subscriber information and pricing have emerged as key issues."
Apple's pricing model for book, magazine, and newspaper publishers is quite similar to what it uses for songs in the iTunes Store. Publishers of the content get a 70 percent cut, and Apple keeps 30 percent as payment for infrastructure costs and providing the service.
Apple also gives publishers some control over pricing, but that's not enough for the newspaper and magazine industry. Industry publishers told the Financial Times that "the revenue-sharing plan makes less sense for recurring charges such as subscriptions."
Another key issue is with subscriber information. This is something newspapers have kept for themselves since the industry began tracking its customers. Newspapers use those demographics in a numbers of ways, including marketing and subscription trends, among other things.
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It also says:
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In other news, the Los Angeles Times says Apple will offer publishers use of its FairPlay digital rights management technology to protect digital books and other publications. DRM is used in the digital media industry to deter piracy and copying of materials.
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You can read all about FairPlay on Wikipedia at:
http://en.wikipedia.org/wiki/FairPlay