I know this is an old post and you might have found the solution already. Just in case you haven't or for anyone coming here for a possible solution, I'll give you my take on it. If you are using a fairly new version of iOS, you would think an audiobook's content would reside inside the 'Music' app on your iPhone, iPod or iPad. It actually doesn't. When you purchase an Audiobook, or if you import it in the correct way into iTunes, the media kind of of your tracks (or chapters) should be set to 'Audiobook' inside your iTunes library. So, when you sync your device with your Mac, your audiobooks will actually appear inside the 'iBooks' app on your portable device, and not in the 'Music' app. Think about it – it's a book in audible format, not a musical album.
If you don't have the 'iBooks' app on your device when syncing your iTunes library, iTunes on the Mac will show a message telling you to install it in order for it to sync your audiobooks from your iTunes library. There is another clue where audiobooks will go on your portable device.
On older versions of iOS, this behaviour is different when syncing from iTunes. As the iBooks app on older versions of iOS doesn't support audio formats, you won't get a message to install the iBooks app. iTunes will just automatically sync your audiobooks to your 'Music' app on the device and they will appear under 'Audiobooks'. It can be found under 'More' (bottom of the screen) when you open the 'Music' app.
I too find it very confusing – especially when you consider the fact that on your Mac, your Audiobooks don't sync to your iBooks app, it ONLY shows up in iTunes. On portable devices (with newer iOS) they show up in 'iBooks' and not in the 'Music' app. It's very inconsistent in my opinion.
