Mike Cane makes the case that iBooks is download-only to avoid potential charges of unfair competition from the EU and/or the Feds:
If Kindle, Kobo, Sony, and others complain, Apple has these lines of defense:
1) We’re all on equal ground with Kindle, Kobo, Sony, etc.
2) Our app has to be chosen and downloaded just like theirs
3) We can show you only X number of iOS users download iBooks
4) We can in fact show you more people use the Kindle app than iBooks!
5) We’re actually disadvantaged — we don’t have a desktop app like Kindle, Kobo, Sony, and Adobe!
6) No one can buy our eBooks unless they download iBooks, period
7) We have no unfair advantage, we’re giving users a choice
There are of course counterpoints to these, but this is exactly Apple's plan; they list the app on the 'built-in apps' page after all, so that's how they see it. It also uses private APIs all over the place, just like App Store apps aren't allowed to do.
However, they do prompt every user who doesn't already have a copy of iBooks to download it each time they visit the App Store. I've seen it myself. And they do have an unfair advantage: they're not paying 30% of their revenue to their competitors.
They are however in the enviable position of being able to mandate that their competitors hand over 30% of revenue to them, apparently unconcerned that most of their competitors keep barely 10% of that revenue for themselves anyway. So it's fine for them to ask their competitors to pay out-of-pocket to have apps on the App Store, never to make any money from them.