It seems the over sensitive Muslim community has been taking offence at recent comments made by the Pope. Pope Benedict XVI made comments in a recent speech how the concept of Holy war is 'contrary to God's plan'.
The Pope's comments are not anti Islam. He was making the point how science and philosophy in western culture have separated themselves from faith, leading to secularisation in Europe.
Secularisation has made it difficult for the West to understand cultures where faith is fundamental.
During his speech the Pope reflected on dialogue between a Byzantine emperor and an 'educated Persian' on the subject of Christianity & Islam and the truth of both. Pope Benedict specifically focused on the distinction between Mohammed's teaching on Jihad & Christianity's view that spreading faith through violence is wholly unreasonable.
I don't see why this would upset anyone? It is a valid point, made well. The use of violence in any form to force someone to conform to your own views is wrong. Violence is incompatible with the nature of God.
You can read the Pope's speech here: