Well, I've actually read the text of Pope Benedict XVI's speech 12 Sep 06.
First I have to say, if it's a rallying cry and a slap in the face for Muslims there are darn few who would or could actually read through the dense language to find it. If there was any doubt that the Holy Father was a professor one only has to try to read this.
Okay. If I read this correctly, there was this Eastern Roman Emperor (Manuel II Paleologos) who was talking with a Muslim while the Muslims were besieging Constantinople.
The Emperor was arguing against forcing conversion by violence. In his argument he said that you must use logic along with your faith to understand the will of God.
Muslims are not required to do that (Islam didn't develop with as strong a Greek (and therefore Socratic) influence and thus to a Muslim God is above and not constrained by logic).
I think the Pope was trying to say that to Christians it is just presumed that logic and faith go hand in hand (although there have been movements to separate logic from theology). It is natural for us. It isn't for other faiths.
The really radical thing that he said (IMHO) is the faiths that do not use logic and faith to understand the will of God are wrong (i.e. Islam).
I can't say I disagree.