The creator of the series wrote a letter to his children explaining what drove him to do it. Here are two notable paragraphs.
I had already made a decision that I needed to find a way to take back Islam from its hostage takers, but I did not known how. The answer was staring me in the face. It was a simple, and as difficult, as the multiplication of 9 by 11: 99. So, at the age of 32, I uncapped my pen to create a concept that could be popular in the East and the West. I would go back to the very sources from which others took violent and hateful messages and offer messages of tolerance and peace in their place. I would give my heroes a Trojan horse in the form of THE 99. Islam was my Helen. I wanted her back.
I told the writers of the animation that only when Jewish kids think that THE 99 characters are Jewish, and Christian kids think they’re Christian, and Muslim kids think they’re Muslim, and Hindu kids think they’re Hindu, that I will consider my vision as having been fully executed.