One of the (imho) most common myths out there right now is that the religions that (heavy quotes) "behave themselves" today, or conduct themselves civilly or what have you, all got to that point through a careful evolution of doctrine that favored more and more benign religion.
Bunk.  One of the most prominent brands of Japanese Buddhism still in existence today is Nichiren, whose doctrines haven't changed since the 16th century.  When they were killing people and dragging the families of political leaders they didn't like out of their homes and beating, raping and killing them.
Proponents of the "Christianity is good, Islam is evil" argument like to trot out the tired old "oh but christianity had a reformation, Islam didn't, therefore Chrisitianity became good and Islam is evil."  As if Christianity as an organized religion, on its own, decided to up and reinvent itself.  Broader secular and sectarian changes, disputes over the doctrine, disputes over the interpretations, conflicts between national monarchs and Rome and a million other considerations all contributed to the forcing of Christianity to re-invent itself to stay relevant.
What's relatively common to "harmless" religions today?  Most of them can be found in prosperous, relatively stable societies with sufficient wealth for people to think about something other than "I could die tomorrow so I better pray."  I suppose that's a kind way to put it.  Another way to put it is that "harmless religion" exists in societies that are safe and spoiled and wealthy and frankly people don't need it.  It's less and less relevant in a daily reality where you spend all day watching TV and checking your cellphone and aren't worried that someone's gonna bomb you and there isn't a thing you can do about it.
What's common to the parts of the Muslim world that create extremists? Autocratic, totalitarian oligarchy where a tiny number of people control, or attempt to maintain exclusive control, of virtually all of the wealth, resources, and power.  And robe themselves up in religion and pay religious schools to teach the rabble that the reason their lives are so shit is because of bad things the West and infidels have done to you.  Meanwhile these same rulers build indoor ski resorts in the desert and manmade resort islands with the money they're making controlling all of the oil resources.  You think these people are really motivated by their Islam, any more than George W. Bush received a phone call from God in his head that told him to invade Iraq (a secular country that iron fisted its religious extremists)?
Anyone who looks back on history and thinks that conflict can be primarily understood as something that isn't a) power b) wealth and control of resources, and thinks instead it can be understood in terms of looking at the doctrine of this religion to understand how it was evil or that religion to understand how it was goodly, is the kind of simpleton rube Machiavelli wrote books to help elites and nobles control and manipulate.