I was referencing the fact that the Ottomans--gradually though not initially--used religion as a means of governance. Under the millet system, the political hierarchy was determined by each ethnic group's religious leaders. In this way, each religion became an intergral part of the Ottoman state. So, any Byzantine bias against Arabs/Muslims was surely converted over the course of 400 Ottoman years to the point that religious leaders in the Ottoman empire sided with the state and against the revolutionary interests of a number of their subjects.

When we talk about the political ideology of one religious group through the eyes of another, we have to also acknowledge one tendency in all religious groups: they all like to remain in power, to demand fealty from their subjects. And that's why Christian leaders under the Ottomans were much more disposed toward an Islamic political regime than they were a Western or European one. Essentially, power is power, no matter the religion and ideology. I'm sure Benedict feels emboldened by the so-called clash of civilizations. He never would have uttered his words in an earlier era.

I should also say that I'm using the term "ethnic" in a much different sense than we use it today. The term ethnic under the Ottomans mainly applies to language use, although even there it's a bit fuzzy as a categorical term. Most Ottoman subjects identified themselves in terms of their religion. You were either Christian, Muslim or Jew. A secondary form of identification was the language you spoke. This second form was malleable however because under the Empire, there were all sorts of incentives to switch religions. Thus, you had Greek-speaking Muslims, and Ladino-speaking Muslims, but you also had Turkish-speaking Christians (the Karamans, crypto-Christians who had simply adopted Turkish as a mother tongue) as well. And I'm not talking about multilingual subjects. They spoke one language exclusively though they did not ascribe to the religion of their dominant language group. At most, the people who are known as Greeks today referred to themselves as Romans. But that distinction began to fall away during the Ottoman period. Hellenism didn't begin until the 17th century.