Why?
Religions are against materialism, against being selfish (promote self sacrifice) and short-sightedness (promise afterlife).
It's no surprise there is so much propaganda against religion. Troll farms of the shadow government and journalists hired to do propaganda such as in Operation Mockingbird are doing their best to manipulate the public discourse so that we hate religion. So that we think religion causes ignorance and intolerance. So we stop studying the prophets. So that we stop having organized communities (churches). They almost succeeded, but we have woken up. We now know their objective is to control us all with money and that to do that we must be all divided, ignorant, selfish, materialistic and shortsighted. We know now they spend billions to accomplish this by deception.
Religions teach the golden rule! Blaming intolerance on religion is like blaming ignorance on education.
We often try blame others for our wrong doings. Of course religion has been blamed for them time and time again. People will use any excuse or false reasoning they can to manipulate others. Of course religion has been used for this. Does that mean religion is to blame? Of course not! Just like science is not to blame for the Tuskegee Syphilis Study.
Religions are a commutation of generations of culture and writing. Of course all sorts of nonsense and inhumanity are mixed in, simply because it has the whole bag of our past culture. The thing is that religions evolve, just like culture evolves and it is up to US to improve them by leaving behind that which is not constructive or good for peace while keeping and adding that which promotes peace and brotherhood of mankind.
Simply by telling one new person every day that now EVERYBODY can live a life of luxury in a Resource Based Economy, we will end terrorism, war, poverty and create a sustainable and just future.