What’s the difference between a catholic (or any deist) saying “you shall not kill” and an atheist saying “you shall not kill”?
In the first case the justification, in too many cases, ends at “it’s god’s will” or some derivation thereof. In the second, for however flawed it may be, the justification is based on reasoning. The first requires you to have faith, and I can’t tell you how many arguments I’ve had with local religious figures where that’s their final statement. The second allows you to disagree and challenge the validity of the statement. The first encourages you to believe, the second to think and judge continually.
This becomes very dangerous when you have a class structure. Anyone can argue in the second case, reason and thought are not restricted by class or privilege (though granted, their accessibility and reach may be). And if you are open to reason then being wrong is nothing more than seeing the greater logic of your opponents argument. But in the first case, you are led. As the leaders of your faith interpret the words, writings, and laws you follow so must you adopt their interpretation or risk being exiled. Those interpretations are combined with the leaders motives (there’s your politicizing religion – I need votes, I’ll appeal to my [fill in the religion] brethren by pitching how strongly I’ll defend our core beliefs against non-belivers; though sadly it seems everyone does this religious or not) are part of the reason there are so many divisions of faith, including extremists.