I've heard those stories before, but I've never experienced it myself. I understand that in countries where there is no division between church and state, that persecution because of personal beliefs is accepted. The reason why, I believe, is that religion is a method of social behavioural patterning and conditioning, and just one person in that culture expressing their own views may get a following that has the capacity to overthrow their system of governance, and cause deterioration to the quality of life for the rest of the inhabitants of that region. What I'm trying to work out, is the sociological ramifications of a society of individuals, of individual beliefs. In short, I'm trying to understand the religion of atheism... because, when defending atheists from religion, I encounter the same arguments... but strangely, when defending religion from atheists, I'm also up against the same debates... which were pretty much the ones that you put forward, predominately "they persecute us as a group"... but I've never encountered that, personally... I tend to get an "Oh well, you're going to hell. I got better things to do" attitude...
It's hard for me to express in words what I'm trying to learn... but Winston Churchill once said, "a fanatic is someone that can't change their mind, and won't change the subject"... Is it just fanaticism that drives the conflict... or is it the difference of faith between the differing sects of religions of sentient god, and non sentient god?

@Dreegle Dude, this quote from you "I believe, is that religion is a method of social behavioural patterning and conditioning, and just one person in that culture expressing their own views may get a following that has the capacity to overthrow their system of governance, and cause deterioration to the quality of life for the rest of the inhabitants of that region." is kind of terrifying.. Do you really think that? One person is going to deteriorate life for the rest of the population for expressing ideas that are contrary to the religion that is being imposed on people?

@thinkwithme I suppose, it is terrifying... but it's also history. The innovative thought of individuals has manipulated society since civilisation began... but we only remember the ones that were right. In religious context, Moses, Jesus, and Mohammed are the individuals that manipulated societies... Non religious, and the arguments against them would be Da Vinci "if god had wanted us to fly, he'd have given us wings", Gallileo on heliocentricity "The Earth is the centre of the universe", Magellan on flat earth, "I have seen the shadow of the earth on the moon"(citation needed that he said that)... The best example of one that was wrong, would be Adolf Hitler (or the organisation he was a puppet of.... There is evidence to suggest he wasn't pulling the strings)... Irrespective of "right", or "wrong", those individuals, with their individual beliefs, changed the world as they knew it, to what we know it as now.