Recently I saw the Finnish film Forbidden Fruit, a movie about two girls from a conservative Lutheran sect who leave the confines of their family and community and explore the wider world. While one girl wants to break taboos such as no make-up, alcohol, television, and sex, the other is there to make sure her friend doesn't go too out of control.
While some of the religious talk I found downright laughable, like a priest describing desires as the devil trying to tempt you (when you're going to personalise nature to that extent, it becomes very silly), my main objection about that way of life was that it was the suppression of autonomy for the sake of doctrine.
There's no introspection, no reflection, just "thou shalt not" as the behavioural framework behind which failure to do so means eternal hellfire. To not even permit a freedom of conscience, at the same time as laying down mental trappings to prevent one from doing so, is something I find unconscinable.
This is not to dismiss why such trappings are laid down, it's hard to think that the reason is anything other than for the perceived best intentions. The consequence of hellfire, if true, is reason enough to bring people into line with what will prevent that horrible outcome. As well as ostracising those who have rejected it for they could lead to the damnation of others.
No matter the intent, the outcome produces a failure of choice, a triumph against the will. It's not giving people the opportunity to choose, it's making the choice for them as to how they should live their life. When it gets to the extreme where the shift away from the heteronomy means being ostracised then the system itself represents a threat to the notion of liberty and autonomy.
I don't want this to be taken as autonomy at all costs, or that anyone can be (or ought to wish to be) truly autonomous, or that someone can't be religious and still have more autonomy than someone who isn't. The problem is that totalitarian practice, the triumph over thought and behaviour, that is something that ought to be rallied against.
The difference can be illustrated with the notion of vegetarianism. Consider two different people who are vegetarians. One is vegetarian because she thought about the consequences of eating meat; for the animal, for her body, for the environment, and came to the decision that she should be vegetarian. The other is vegetarian because he was brought up being told that it was evil to eat meat, that if he ate meat it would come back on him in the next life, etc. The difference between the circumstances should be obvious, the woman who was vegetarian was so by choice, while the man didn't get to make a choice in the matter.
And that is the key. Because while both have the theoretical ability to go to a restaurant and order a steak and both have the moral concern that eating meat is wrong, only the woman can be said to have made a choice. For me as an observer, I can respect the woman's moral position but not the man's, because while I personally disagree with that moral dictum I know that the woman is doing it out of self-determination while the man cannot do so in any reasonable sense of the word choice.
Likewise I don't see a problem of someone being a believer for the quality of having belief. Again while genes and upbringing mean that there's no true autonomy, there must be a recognisable difference between a critical evaluation of one's beliefs and learning how to defend one's beliefs from critical evaluation. The difference between losing the faith and losing the faithful, the difference between choice and enforced conformity.
The current outcry against religion is in-part for me rooted in Enlightenment values. While some wax poetically in almost Utopian fashion about the joy of a society without religion, the main thrust is that threat of the destruction of autonomy. It's the removal of one's right to be able to choose that to me embodies the outrage and the need to be vocal. It's to defend those basic rights in the face of an opposition who wishes to take those away.