Hi,
I struggled with this issue, too, as I started using iBooks Author a while ago. From what I've learned, the ability to offer adjustable fonts for the reader / end user is based on the original template that we built our book on. But there's more as we have choices in e-pub template versions and the Multi-Touch ones included with iBA. I am building a Multi-Touch iBook that is based on the included iBA template for landscape layout—there's no support in that one for the reader to change the font. I found that, for me, I had to choose between: fixed layout, reflowable layout, and Multi-Touch (exclusive to iBooks). Given that the Multi-Touch feature is most important to me as my iBook project has a lot of nested gallery widgets, the lack of adjustable fonts was acceptable (for me).
I know there are online articles somewhere at Apple but I couldn't readily find them. I did find this other article that may help you:
http://ebookarchitects.com/learn-about-ebooks/non-fiction-fixed-layout/
Best Regards and don't give up ;-)