I just watched the recent film "Agora" (starring Rachel Weisz), which deals with Christian riots in Alexandria in Egypt in the 4th century AD. This kind of film powerfully shows how, throughout the ages, Religion has been used by demagogues and fanatics to silence free thinking and rational thought. The rise of Christianity came about partially as a response against the decadent poytheism they saw in Rome; the rise of Islam came about under a very similar social environment in Arabia. One side-effect of this was that learning became skewed through a narrow-minded lens of thought; if it was written in "the book", it was good; if it was not written, it was bad.
I'm not going to spend my time criticising religion here. Any line of thought, whether faith or philosophy, can be misused for someone's own ends. Whereas one religion can be intolerant towards another, the same can be true of those who are not religious - athiesm expressed by some people can be as intolorant of religion as any religious fanatic. Some atheists take atheism to be a kind of "religion" in itself - Communism being just one example. It's not what you believe, but how you show it that's important. I've met a number of devout people during my time as a teacher abroad; I respect any one who chooses to live their life to good ends, but has the respect for humanity to not force their beliefs onto others, or, even worse, makes a show of moral superiority.
The example of the Danish publication of the offensive images of Muhammed is a great example of the divide here. Muslims around the world were horrified and disgusted. Europeans, however, were confused by the Muslim reaction, and some countries published the images as a sign to show how much more open-minded they were compared to Muslims. Iran, in reaction, published anti-Semitic images, to the offense of Europe. But this is the point - the Iranians were consistent with the European mentality. If it is fair to denegrate Islam, why not Judiaism? Why not Hinduism? Why not publish homophobic imagery? For that matter, let's have a competition to publish the most offensive image ever! Racist, sexist, violent, it doesn't matter! In Europe, people want to be indulgently offensive! In Denmark, being "tolerant" means you can offend any person you want to with full support of the state media! Yes, this shows how "enlightened" we are. And if you have a problem with that, then that only shows how "intolerant" you are of other people. Yes, according to this rationale, "morality" is equal to "intolerance".
"Religious intolerance" can have two meanings: a) intolerance of other religious (fanaticism); b) intolerance of religions as a whole. "Intolerance" is quite a flexible term, really. You can be intolerant of intolerance, for example (making you an "Intolerance Intolerant").