Two religions are destined to continually clash. They are not Christianity and Islam. Rather, they are religion as experienced by the individual and religion as experienced by society. What society needs is toleration of others; what the individual needs is separation from, and even rejetion of, others.
Huston Smith points out that he doesn't speak "language" but, rather, speaks "a language." All the talk of religion, of the transcendent, of God and souls ultimately needs a means of expression other than the abstract. In this, the individual has the need for something specific and, in a sense, something custom and true to the self. This kind of religion invariably separates the individual from the community - whether it is a group of Christians who shy away from worldly influences or the individual who loves fellowship within that group while feeling a degree of separation from even his or her group. This role of communing with something eternal - whether it is perceived as touching God, Holy Scriptures, the spiritual, the eternal, or the god within - is necessarily separating. Such a separation invariably includes, or at least connotes, a condemnation of the world or other groups who find their refuge through some other process, intermediary, or belief or even profess no need for such separation.
What the individual experiences as refuge from the world the world quite rightly experiences as rejection. And crudely or thoughtlessly done, it becomes offensive. The pope trying to declare a distinction from Islam very easily slips into condemning Muslims.
There was a time when it was laughable that communities would have to be mindful of their impact on the environment. Nature was so big and people so small that the notion of harming it was inconceivable. During medieval times, people wrote of walking through forests and not seeing sun light for days – walking through forests that no longer exist. When Christ or Mohammed first preached, it may well have seemed ridiculous to their early followers that there would some day be billions of Christians and Muslims whose desire to protect themselves from a hostile world would actually be a threat to that world.
Obviously, religious individuals need to do more to show toleration, to exhibit the side of most religions that emphasizes the love for others more than love for self. Much, but perhaps still not enough, has been made of this. Less has been made of the need for society to become more sensitive to the need of the individual to withdraw from and even reject "the world" as a means for the individual to save his or her soul.