Benedict's real target wasn't Islam.

In The Pope's lecture also shakes Catholic theologians by Bernward Loheide, it is explained that the quotation from a medieval text, which so outraged many in the Islamic world, wasn't directed at Islam, but was at the service of an argument critical of much recent Christian theology.

Benedict's thesis about the relationship between faith and reason has its foundation in ancient Greek philosophy.

However, a sizeable number of Catholic and Protestant theologians argue that this so-called neo-Platonic perspective is inadequate for 21st century theology.

"The encounter between the Biblical message and Greek thought did not happen by chance," said Benedict, who contends that Christianity reflects much of the thought of the pre-Christian Greek philosopher Plato.

Christianity, he said, was a rapprochement between Jewish belief and Greek thought. Faith and reason are in harmony when God is understood as truth, beauty, goodness and universal reason, which are there for all human beings to grasp.

In the world of Christian theology, most competing ideas have been around for a long time. Benedict's ideas can be traced back to St. John the Evangelist whose gospel began, "In the beginning was the logos." Logos is a Greek term that means both reason and the word.

The article goes on to describe why many German theologians disagree with the Pope's argument. Insofar as I understand the debate, I'm with the Pope.

And again, Daniel Johnson in the New York Sun:

So what was the pope really saying in that lecture he gave in Regensburg, his old stamping ground in Bavaria? It was a rich and elegant reflection on the rationality of faith, couched in the erudite language of a very German philosophical discourse.

But the message was, at heart, a straightforward one. The Jewish or Christian God acts in accordance with reason: In the beginning was the Word, the Logos. Benedict emphasizes that this new, logocentric understanding of God is already present in the Hebrew Bible, long before the fusion of Jerusalem and Athens in the New Testament. Our knowledge of God — the God of Israel or the God of Christianity — emerges in the unfolding of the encounter between faith and reason.

The contribution of Hellenic thought to this gradual enlightenment is, for Benedict, essential. He laments the "dehellenization" of Christianity since the Reformation. Its effect, he thinks, has been to "relegate religion to the realm of subcultures" and to treat scientific rationality as if it had nothing whatever to do with faith. "The West has long been endangered by this aversion to the questions which underlie its rationality," he warns. If the West ignores this theological perspective, it "can only suffer great harm."

More: Robert L. Wilken, Robert T. Miller, Richard J. Neuhaus.