The Holy Father thus sincerely regrets that certain passages of his address could have sounded offensive to the sensitivities of the Muslim faithful, and should have been interpreted in a manner that in no way corresponds to his intentions.
On Sunday, he reiterated:
Pope Benedict XVI said Sunday he was "deeply sorry" about the angry reaction sparked by his speech about Islam and holy war and said the text did not reflect his personal opinion.
"These (words) were in fact a quotation from a medieval text which do not in any way express my personal thought," Benedict told pilgrims at his summer palace outside Rome.
Have you read the Pope's comments in context? You should. The entire speech is fascinating, and makes clear that he used the Islam passage in question to illustrate a larger point about the intersection of religion and reason, and the consequences of separating the two. I'm snipping some shorter, relevant parts, but the whole thing is recommended.
This profound sense of coherence within the universe of reason was not troubled, even when it was once reported that a colleague had said there was something odd about our university: It had two faculties devoted to something that did not exist: God. That even in the face of such radical skepticism it is still necessary and reasonable to raise the question of God through the use of reason, and to do so in the context of the tradition of the Christian faith: This, within the university as a whole, was accepted without question.
Benedict sets up his Islam comments extensively. He's quoting a discussion between an "educated" and "learned" Persian and a Byzantine emporer on the subject of Christianity and Islam.
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