Interpretation has always been the biggest problem with this sort of thing. Bin Laden and his kind interpret it all to mean thatnthey must fight and die and kill others for the cause and believe absolutely that their holy texts support them; many more say that virtually the complete opposite is so.
In the end, everyone has to pick and choose what they believe. For example the world would be a complete nightmare if people took the Bible literally (complete with gay burnings and punishments for not selling your daughter into slavery and for growing different crops in adjacent fields (those are from Deuterononmy).
MOST people have the common sense to adhere to the spirit of things but it doesn't take many people to interpret their texts badly to form a higgly unpleasant organisation like Al Qaeda.
Raz, your point about the IRA never being labelled as Christian terrorists is taken, but it's not just because of western prejudice; it's because the IRA (and even the Loyallists) don't quote bibilical lines all the time supporting their views and glorifying their position, at least not in public. Muslim fundamentalists, which I whole-heartedly accept are massively mistaken and unrepresentative, DO do such things.
Hence people have associated these terrorists with their religion in a way they have not associated terrorists in Northern Ireland with theirs.
It's sad, I know, and it's people like you that often have to take the fall out for it, but that's why, I think.