The margins are unacceptable the way they are in those apps.
But equally annoying is, indeed, the arrogance of the assumption that "one size fits all".

"We're gonna set your margins for ya, folks, and you can just put up and shut up. Take it or leave it. We don't give a damn about what you find pleasant or useful while reading books. We're here to
sell you books, not to make the
reading of those books pleasant or useful for you. That's of
secondary importance to us -- in fact, we couldn't care less about
that, and we're only going through the motions of caring about it, because that's what our PR strategy demands."
This
contempt for the user, for the reader's needs and preferences, permeates both iBooks and the Kindle app. It's not just about page margins -- the same neglect is there for pretty much every feature you might expect out of an e-reader in 2013. Which is why iBooks and the Kindle app are such lame, bad-quality e-readers, and unusable for me.