Trying to get back to Undesired Walrus and the OP,
"..Despite my desire for religion to see itself for the falsehood I believe it to be, my most pressing desire is for it to be treated with the same respect I give a political opinion.."
I agree with this statement completely. That is my most pressing desire, too.
I think that you are missing something, though, when you compare religious beliefs to homosexuality or military life.
The thing that is missing from your comparison is the understanding that most people are born into their religion. It not only informs their day to day behavior and understandings, but it informs their social standings and social interactions as well as their entire worldview and sense of self. Even if you are not born into a particularly religious family, the religion of your society informs and influences your sense of self.
If I were going to compare it to something, I think it might be more appropriate to compare it to something far more fundamental to a person's worldview, like heterosexuality and stereotypical gender behavior, or perhaps to race. Almost from the day we are born we are inundated with social ideas about "boys behave this way" and "girls behave that way". Or "white people do this" and "brown people do that". These messages, which we are programmed to blindly accept, not only come stated verbally by people in authority over our lives, but unstated by the behavior and actions of those people we love and mimic; our parents, family members, community members and leaders.
I think for a person to realize that their religious beliefs are just that, - beliefs, no different in importance from anyone else's beliefs takes a huge shift of worldview. Similar to a person realizing that they are a homosexual. Or a person realizing that they have been guilty of racism. It takes acknowledging that how you were raised is not necessarily "The Truth", the world is different from what you thought, and that other ways of being exist. It takes acknowledging that the people you love and admire, who have raised you and cared for you, and done a darn fine job of it, just might have been wrong about things. Important things. It takes a lot of bravery to make that shift.
I think the strength of homophobia and racism still in even the most civilized of nations is a testament to how many people are not willing to make that shift. We don't like to have to rethink our worldviews. And we really resent it when "others" tell us we have to.
We are a clannish and cliquish species. We often have herd mentalities. We tend to first define things as "us" and "them". We tend to jumble nationalism, patriotism, religion and race in our brains. It is so deeply ingrained in our psyches that we have a hard time separating them out. We don't think about "who" a person is first, we usually try to define "what" they are. And each "what" we come up with (gender, race, sexuality, religion, nationality, political affiliation, etc.) is a value judgement.
So, in thinking about how we can actively help people to make this shift of worldview, I personally believe it is better to concentrate the conversations on individual laws or individual events on which we wish to exert change and let individuals work out for themselves how the ramifications of these conversations are justified within the context of their social identities, rather than making broad statements that work to offend large groups of people and encourage a defensive "us against them" attitude. I think we get much farther discussing why we as individuals shouldn't burn down embassies rather than the religion of people that burned down an embassy.
Yes, you may have the right to publish a picture of poo on a scripture, but I would question your motives for doing so. And I would question whether your publication of that picture did anything to move us toward more peaceful negotiations, toward better human rights, toward more equitable trade negotiations.. toward any of what I consider to be our higher goals.
We all self-censor every day. And honestly, I question the motivation of some who declare that an appropriate response to muslim indignation is to create and publish even more material that muslims might find offensive, in the name of "free speech" or "fight against censorship". If one really wants to make a point about free speech, why not publish something that would be considered almost universally offensive? Why not publish cartoons depicting humorously the murder of children, or the funny torture of kittens? Why not publish cartoons depicting the owner(s) of your newspaper doing these things? Or yourself? Why not lead by example and make the point about freedom by publishing something we ourselves find offensive, then dealing with the fallout in a peaceful manner?