1. The Pope gave this speech to European secularists knowing full well that Islamic extremists (that is, a sizable portion of Muslims in both Europe and the Middle East) would react to the speech in an uncivil manner. Their uncivil reaction would highlight to those European secularists who heard the speech or read it that the secular European world and the Catholic intellectual world share something in common that is not shared with them by the Islamic world in general - civility and a cultured intellectual reserve. By highlighting this the Pope suggests in a subtle manner that this shared civility may just have something to do with a common intellectual heritage - the synthesis of Christian and hellenic thought which is found in the intellectual patrimony of Europe.
2. If "1" is true then we might view the Pope's speech as a brilliant rhetorical devise used to attempt to reestablish a common intellectual bond between the European university (or European intellectuals in general) and the Catholic Church in the midst of a Europe which is increasingly being Islamicized. This is a very subtle way for the Pope to remind Europeans that even as secularists they have more in common with Catholic Christianity than they do with Islam. This may seem an obvious point, but in today's Europe it is not - many secularists instinctually feel some resonance with Islam due to their shared hatred of Christianity. Thus if one can present Christianity as a reasoned, intellectually reserved and cultured form of thought which is quintessentially European at the exact moment that the Muslims in the midst are waving their "death to the infidels" signs then one has just effectively changed the former "us vs. them" to a new alliance of "us vs. them." I believe that this is exactly what Pope Benedict intended with this speech.
Read it all.