My model of this situation is less sanguine than others here, though Yvain and Tetronian hinted at it: it's identity politics. Humans very naturally associate themselves with many different groups, some of them arbitrarily defined, and often without any conscious thought. Religion, favorite sports teams, the street/neighborhood/city/state/country you live in, and many other things can be the focal point of these groups. The more you associate with one of these groups, the more its part of your identity - i.e. how you see yourself. If you associate with one of these groups particularly strongly, any action which appears to make a rival group look better will personally offend you and elicit a response.

I'm from the St. Louis area in Missouri (US), and our baseball team, the St. Louis Cardinals, has a longstanding rivalry with the Chicago Cubs, a nearby team. In the past (when the Cubs were fairly good and actually a threat), I've seen Cardinals and Cubs fans get into fights for no other reason than one of them insulted the other's favorite team. I've heard similar stories about fans of St. Louis and Chicago's hockey teams (another rivalry). I had a philosophy professor in undergrad who would get visibly upset at times in class when arguing against reductionism (he's Christian), and I think we've all seen both religious and political debates get heated.

My model of all these situations is the same as my model of your situation. Before joining LessWrong, you spent a certain amount of identity points on "being rational," but probably didn't have much of a group to identify with, so when someone who's religious or superstitious got in a jab against their hated rival, the rationalists, you didn't feel anything or think much of it. Now that you've been a member of LW for some time and absorbed its memes, you're spending many more identity points on "being rational" primarily because, I conjecture, you now can point to a large, dedicated group of like-minded people. As such, you're much more likely to react with offense when someone brings up religion or homeopathy in a positive light, since that's implicitly an attack on your group.

Identity actually terrifies me because of how it seems able to control my actions and even my beliefs. I remember writing a political philosophy paper in undergrad and actually thinking "but if I use this argument, then I can't argue for Anarcho-Capitalism anymore." If that wasn't a red flag, I don't know what is - though naturally I didn't notice it as one at the time. One way to deal with this is to keep your identity small so that you minimize how often you're swayed in one direction or another for reasons purely of identity politics. Also, crafting a particular identity for yourself can work. I try to think of myself as curious and tolerant of beliefs that I know to be crazy.

My own experience has been similar to badger's - I've grown more tolerant of crazy beliefs (and beliefs that simply contradict my own) since discovering OB/LW. I can't really be sure about why, but I'd like to think it's because I've implemented the two strategies above. Learning that politics is the mind killer and realizing that this applied more broadly than groups based on political affiliation actually scared me to some extent. My immediate reaction was to reject all group affiliations (that I could anyway), but since then I've let some of the more innocuous ones back in because I'd rather consciously spend my identity points than let my brain subconsciously do it.