This has to at least annoyed the pope if not really made him feel that as the leader of all cathlolics it is his duty to speak out. He did. But any apology or attempt at clarification is a mistake considering who he is dealing with.
Here is the official statement released by the Vatican's Secretary of State, Cardinal Bertone.
IMHO, the most pertinent parts are (emphasis mine):
"- As for the opinion of the Byzantine emperor Manuel II Paleologus which he quoted during his Regensburg talk, the Holy Father did not mean, nor does he mean, to make that opinion his own in any way. He simply used it as a means to undertake - in an academic context, and as is evident from a complete and attentive reading of the text - certain reflections on the theme of the relationship between religion and violence in general, and to conclude with a clear and radical rejection of the religious motivation for violence, from whatever side it may come."
"- The Holy Father thus sincerely regrets that certain passages of his address could have sounded offensive to the sensitivities of the Muslim faithful, and [could] have been interpreted in a manner that in no way corresponds to his intentions. Indeed it was he who, before the religious fervor of Muslim believers, warned secularized Western culture to guard against 'the contempt for God and the cynicism that considers mockery of the sacred to be an exercise of freedom'.""- In reiterating his respect and esteem for those who profess Islam, he hopes they will be helped to understand the correct meaning of his words so that, quickly surmounting this present uneasy moment, witness to the 'Creator of heaven and earth, Who has spoken to men' may be reinforced, ..."