The problem with this argument is that the label of religion still servers a useful purpose. It lets us know right away when an idea is wrong. Religion is not just wrong, but uniquely wrong. It is always wrong. It's the true north for your mental compass, the absolute zero of your belief barometer, the nobel gas in your idea-chemistry set.
Example: I am not a world renowned physicist. I'm somewhat familiar with it as an interested layman. If a new quantum model were to show up on the news explaining how neutrinos are still going faster than light, I wouldn't be able to personally vet the theory. If I wanted to find the truth, I could ask people on LessWrong what they thought or seek out expert opinion elsewhere. However, if this new quantum model was based on divine revelation (or hey, lets go with angels), I would immediately know it was incorrect. This same heuristic holds true whether I'm looking at cancer treatement options for my parents, choosing what of physical therapy message to get or not get, trying to find a nice personality test to take, or learning my girlfriend became pregnant via immaculate conception.
So, why treat religion separately? Because it is useful having a unique category for 'always wrong theories' . It saves me time mentally filing newly encountered information. As for special protections for religion, I think it works out quite well for us. Considering we're considered worse than rapists, I shudder to think how we would be treated if there weren't a precedent for religious tolerance.
Ramanujan claimed to get mathematical revelations from the Hindu goddess Namagiri. Some Hindus today actually believe that Ramanujan really did get math from deities.
This isn't the only example of this I have, only the most blatant. The Bible has rules about covering up feces. The Talmud has one wash hands before eating. And it also says not to use sharp sticks or rocks when wiping. If you want I can give similar examples from Islamic texts.
Your claim that " Religion is not just wrong, but uniquely wrong. It is always wrong." seems to not work.
I've recently run across this 2007 post on the blog Unqualified Reservations (archive best read here). It is written by Mencious Moldbug, who is probably familiar to some Overcoming Bias and Lesswrong readers. He is a erudite, controversial and most of all contrarian social critic and writer. In 2010 he debated Robin Hanson on the subject of Futarchy.
Violating Godwin's law to breach the fence between religion and ideology to see what cognitive dissonances we can dredge up is old hat for us LWers (A Parable On Obsolete Ideologies 2009 by Yvain).
I hope you can now see reason I've picked a partially misleading title, since I think Moldbug makes a pretty convincing argument that belief in "religion" may be considered harmful even for atheists, let alone those of us who aspire to refine rationality.
In such a model questions like "is the Church of Scientology a religion?" dissolve rapidly. Whether something should be tax exempt because it is "really" a "religion" or "a church" is a legal question of importance only to activists trying to challenge law and lawyers, that shouldn't change our ethical intuitions or cause us to try to imagine a sea or play up rather minor geographical features, to separate the continents of Religion and Ideology in our maps of reality.
Every single proposed mechanism for the retention and spread of religion from convenient curiosity stoppers, indoctrination of youth, to tribal identity markers hold for ideology just as strongly as for religion. Even seemingly very specific memetic adaptations like "God of the gaps", seem to arise in various non-theistic ideologies. Maybe similar adaptations arise because it is the same niche?
Thinking about the implications of such a hypothesis, atheism for one additional god is a rather easy step of rationality to take. Very few people believe in the great Juju or Zeus. Adding YHWH to the list isn't that much of a stretch, for those fortunate enough to be educated and living in most of the West.
But how hard is it for someone to question, in a unbiased fashion, such gods and holy words such as say Democracy?