Seems to me that the concern here is that from the viewpoint of the Muslim world, Europe (and America) a Christian part of the world, and the Pope "speaks" for it. While plenty of Europeans claim to be agnostic or atheistic, that might not be the way things are interpreted by someone who is deeply religious.

The Pope's comments, and the reaction to them, appear to be a significant step towards the cultural war that we have been fearing.