The Catholic Church has always been against bigotry toward any human based on so called race or religious beliefs. People otoh are a different story, religion does not hurt people, but people hurt people. That has really alawys been the case just like it is with guns, and other devices even fast food…you dont have to eat fast food but some people eat so much fast food that it causes health problems. People also dont have to be terrorists but some people choose to be terrorists.
During the Crusades our Saint Francis of Assisi meant with the Sultan of Egypt…Saint Francis being the remarkably nice man that he was…was able to get the Muslims to peacefully cede Jerusalem back to the Christians. We saw Just war in WW2, when Muslims and Christians teamed up to fight ISIL. We have seen throughout the middle ages Muslims and Christians joining forces to fight a common enemy. The enemy of Christians has never been Islam, it cant be because of how Muhammad made treaties and viewed Christians as full equals to Muslims. Historically speaking, there has never been a time when it was Islam vs the world or Christianity vs the world.
You talk about Just war, well could you imagine my friend if someone in the media labeled the KKK terrorists as followers of Just war or holy war? I blame some of the media in part for why a few folks have negative views of Islam. During the rise of the KKK, media outlets rarely if ever talked about how radical Christians were the problem…well today a few folks in the media are using words like Jihad, or Islamic to describe terrorist groups like ISIL…this creates a negative image of Islam in the minds of some folks who might not know Muslims in real life…or only know about Muslims from a media outlet which claims that ISIL is Islamic while not providing coverage to the Muslims who team up with Christians to take Jihad to ISIL.
It does seem though that more and more people are seeing ISIL, Taliban, Boko Haram for what they are…terrorist groups that go against religion.