Pretty much every updated Apple app seems to be getting hit hard in the App Store, except Keynote. What's interesting is that only the iBooks app's bad reviews are predominantly about the new look.
Well, bookworms as a whole do tend to be a bit conservative. I remember when ebooks first started. Most of my reading friends were convinced that giving up paper books would ruin the entire reading experience. I bet the same thing happened when bound books started replacing scrolls. The crackle of rolled paper, the smell of papyrus, the beauty of continuous text; none of that inconvenient page turning nonsense.
Me? I do like paper book, especially nice leather bound editions, and I kind of liked the wood shelves in iBooks, but in the end the only thing I really care about is that whatever I'm holding goes away once I start reading. I'm there to experience the story or absorb the information. Paper, old iBooks, new iBooks; they all pass that test.
I'll also add that I haven't been experiencing most of the problems that reviewers are blasting the other products with. Either I"m lucky (which happens sometimes), or the general outrage at change in general has those who do experience problems far more likely to take the time to write a review. Plus the bugs that plague any big update.
Hold in mind that the iWorks apps have never had top ratings in the App Store. From what I can see that's mostly because many people buy them thinking they will be full MS Office replacements, and work exactly the same way. They aren't. They don't.