I really don't have anything new to say about the Muslim anger over what Benedict said; I will merely reiterate that he cited one dialogue between an Emporer and a Muslim that touched on the nature of God and reason, and that he did not try to make that Muslim a representation of all of Islam. For the best (from what I've seen) source on what the Pope really meant, go here. (HT: Amy Welborn)
Now as fun as it is to pontificate on faith and reason, and the clash of civilizations or lack thereof, Christians in the Middle East and North Africa have been sorely pressed for a long time, and if it wasn't this statement of Benedict that sparked the current round of church-burnings and shootings, it would have been something else in the near future.
I urge you to support groups like CNEWA or Aid to the Church in Need; I know from personal experience that you can set up monthly automatic donations with CNEWA (either a general donation or a specific sponsorship of a child, seminarian or novice religious).
Importantly, CNEWA also helps education Americans about the Eastern Churches–it may be surprising to many Republicans that some Palestinians are Christian, and they are getting the greasy end of the stick from Muslim and Israeli alike.
CNEWA's ecumenical outreaches may mean that they'll be helping the Orthodox Palestinians rebuild their churches that were damaged in this most recent outbreak of violence.