Nobody in these forums can tell you why Apple does this, but of course you can ask for a change via
http://www.apple.com/feedback
Apple itself does not consider that iBooks Author supports Arabic correctly. Arabic is on the list of languages where Apple requires the epub3 format, which neither iBA nor Pages can produce. Other languages on the list include Chinese and Japanese.
Arabic is also not the only language which the iBookstore is not yet ready to support for some reason. Others are Amharic, Aramaic, Burmese, Persian/Farsi, Hebrew, Khmer, Lao, Malay (Jawi/Arabic), Sinhala, Tamil, Urdu.
My personal guess is that Apple does not yet think the iBooks app can display books in these languages with the quality level they want to have in their store.
The bottom line is that in the meantime you have to try to exploit this market via other stores like Kindle, Nook, Kobo, Googlbooks, Sony.