There are good arguments for why a rationalist should distance him or herself from anti-religiousness (distinct from atheism), but the irrationality of others isn't one of them.
Even if you start from the presumption that religion is a social evil, it doesn't necessarily follow that you should be anti-religious. If you start from the presumption that religion is a social evil, you should operate on the mechanisms that abolish religion, rather than the mechanisms which signal your opposition to religion. This may mean encouraging critical thought; it doesn't mean claiming critical thought will lead to atheism.
Presuming somebody is religious, at best, the claim that critical thought will lead to atheism is going to lead to their looking for flaws in your reasoning. People's ability to rationalize is directly proportional to their capacity for reason, so they'll probably find them, whether or not they exist.
So I have been checking laws around the world regarding Apostasy. And I have found extremely troubling data on the approach Muslims take to dealing with apostates. In most cases, publicly stating that you do not, in fact, love Big Brother (specifically, that you do not believe in God, the Prophet, or Islam), after having professed the Profession of Faith being adult and sane (otherwise, you were never a Muslim in the first place), will get you killed.
Yes, killed. It's one of the only three things traditional Islamic tribunals hand out death penalties for, the others being murder and adultery.
However, interestingly enough, you are often given three days of detainment to "think it over" and "accept the faith".
Some other countries, though, are more forgiving: you are allowed to be a public apostate. But you are still not allowed to proselytize: that remains a crime (in Morocco it's 15 years of prison, and a flogging). Though proselytism is also a crime if you are not a Muslim. I leave to your imagination how precarious the situation of religious minorities is, in this context.
How little sense all of this makes, from a theological perspective. Forcing someone to "accept the faith" at knife point? Forbidding you from arguing against the Lord's (reputedly) absolutely self-evident and miraculously beautiful Word?
No. These are the patterns of sedition and treason laws. The crime of the Apostate is not one against the Lord (He can take care of Himself, and He certainly can take care of the Apostate) but against the State (existence of a human lord contingent on political regime).
And the lesswronger asks himself: "How is that my concern? Please, get to the point." The point is that the promotion of rationalism faces a terrible obstacle there. We're not talking "God Hates You" placards, or getting fired from your job. We're talking fire range and electric chair.
"Sure," you say, "but rationalism is not about atheism." And you'd be right. It isn't. It's just a very likely conclusion for the rationalist mind to reach, and, also, our cult leader (:P) is a raging, bitter, passionate atheist. That is enough. If word spreads and authorities find out, just peddling HPMOR might get people jailed. And that's not accounting for the hypothetical (cough) case of a young adult reading the Sequences and getting all hotheaded about it and doing something stupid. Like trying to promote our brand of rationality in such hostile terrain.
So, let's take this hypothetical (harrumph) youth. They see irrationality around them, obvious and immense, they see the waste and the pain it causes. They'd like to do something about it. How would you advise them to go about it? Would you advise them to, in fact, do nothing at all?
More importantly, concerning Less Wrong itself, should we try to distance ourselves from atheism and anti-religiousness as such? Is this baggage too inconvenient, or is it too much a part of what we stand for?