It's interesting that a passing comment in the University of Regensburg (of all places) could incite such a backlash. When the Pope referred to an ancient Byzantine Emperor's quote linking Muhammad with evil, it set off a fury across the Muslim world very much like the fall-out from the infamous Danish cartoons.
Churches were attacked in the West Bank, there have been demonstrations, and the Pope reviled as another Hitler or Mussolini, despite his numerous apologies and calls for talks with Muslim envoys.
I don't support preaching intolerant messages, I don't support the US-backed Israeli policy in the Middle East (from 'security barriers' to bulldozing homes to the excessive use of force) and I definitely don't support the Pope or the Vatican. But why should Islam be immune to such attacks that can be launched at all other world religions? Christians and Jews are often criticized in less than flattering terms as infidels, crusaders or worse.
The way to fight such intolerant ideas is not to pretend they don't exist and ban these "taboo areas" from freedom of speech and the public domain, but to allow them to enter the free marketplace of ideas where they will be rightfully denounced, criticized and eventually discredited. This doesn't mean minimizing the offence taken, which is entirely justified and shouldn't be overlooked. But reason and peace must win the war over unchecked passion and violence. Just look at Martin Luther King, Gandhi or Nelson Mandela's struglle against apartheid - the hearts and minds of the world were won over by mass demonstrations, largely peaceful resistance and a patent sense of injustice.
Truth has nothing to fear. There are so many Muslim scholars are calling for exactly that - openness, reform, renewal and self-questioning. Indeed, if Islam is to be a religion of peace, it will win over hearts and minds by truth, reason and debate, not violent reprisals in the street.