Are your fonts encrypted? See if you have an encryption.xml file inside the META-INF folder. Delete it an try to load the ePUB again in iBooks. Also, make sure you're using OTF, TTF or SVG fonts. Postscript Type 1 fonts aren't supported.
iBooks documentation says that it supports IDPF's Font Mangling (the default method in Indesign CS6 to encrypt fonts), but I had no luck with it in iBooks 2.2.