The ability for the reader to change the font size in an ibook created with IBA only works if the book is one that was designed to be viewed landscape or portrait (like all the templates available with iBooks 1). However, with the new portrait templates in ibooks 2, that feature is not availble. In other words, an ibook designed with a portrait-only tempalte will not provide the user with the ability to change font size.
So, if you really want you readers to be able to change font size, you need to use a landscape template and design it as a portrait book However, since you won't be able to disable the landscape view, you'd have to have a notice at the beginning (e.g. the intro media) to let them know to rotate their ipad so they can change font size.