"Yesterday a French Muslim was interviewed on French TV and stated that although he was deeply offended by the Cartoons he did not condone the Terrorists actions. I could compare this with the IRA in the 1970's. Many agreed with the cause but the majority or Irish Catholics berated the manner in which the IRA publicized it. "
The IRA's cause was more accurately associated with Irish Republicanism, not Catholicism. It was always an important principle of the former that, however idealistically, it was not specific to one religion. Of course in practice Catholics identified with it more but that was for political reasons.
So when we come to compare the IRA campaign with acts by jihadists etc we are perhaps on firmer ground if we compare the distinction made (or not made) by others when reacting to it. For example the "tarring all Moslems with the same brush" attitude of counter-extremists nowadays, and the "let's go and kick a Catholic" response by Ulster loyalists of the time.
Discussion of the religious aspect, if there is one, is not necessarily the best way to approach this. Nor to be honest, is the "war on free speech" angle.
More appropriate newspaper headlines would be
"Same old intolerant *** happens yet again". But then that would be a lot duller