You're not crazy.
I, too, tried to get iBooks on my MacBook Air (OS X 10.9) to sync some homemade PDF's to iBooks on my iPad 2 (iOS 7.0.3) and never did figure it out. However, Kindle for iPad can handle PDF's just fine, and I was able to push my files from the laptop to ipad using iTunes (11.1.2) without any problem. This is with the iPad connected directly to the MacBook Air with a cable, not wirelessly. Then I could view my PDF's with the Kindle app.
Not the solution you were looking for, but a pretty good workaround.
Progress! I have just put a new pdf into iBooks on my Mac and this is showing in the Books heading in iTunes when my iPhone is connected.