It is therefore timely for our shrewd and intellectual Pope to warn at Regensburg of the danger of de-rationalization of faith (leading to fideism, one of the by-products of the so-called "Reformation"). The pope made two points about the malady that the modern world faces from the separation of faith and reason:
1. "only the kind of certainty resulting from the interplay of mathematical and empirical elements can be considered scientific", and
2. "[it] excludes the question of God, making it appear an unscientific or pre-scientific question."
The part that offends a large part of the Muslim world, ironically, was a quote that illustrated exactly the absence of reason in faith, as the Byzantine Emperor (and also, the Pope) saw it: the view of a transcendent God in a particular school of thought in Islam justifies (and explains the tendency for) violent (irrational) means to spread the faith. If God does not honor reason, then it follows that nothing need to be rational (and nothing could be irrational) when it comes to matters of faith. This article dug up the history of reason within Islam—I could understand why, in Islam's history, advocates of reason was suppressed (perhaps out of fear of rationalism?): Islam has no equivalent of the Church's Magisterium to guard against potential heresies.
UPDATE: John L. Allen Jr. cautions against sound-biting an intellectual German professor's discourse and sees the pope's speech as an invitation to a frank dialog with Islam.