I was surprised at this food-fight, since these folks normally get along quite well, and all read each other's stuff. But I can kind of see why the "rationality community" might rub some people the wrong way. Here are my hypotheses:
1. The name
The members of the "rationality community" call themselves that because they spend a lot of effort trying to be more rational. But to an outsider, the name sounds like a claim that the community has already attained perfect rationality. If that were true, it would imply that the community's conclusions should be treated with extra reverence, or even as received wisdom - kind of like we take physicists' word on physics results. In other words, the very name of the "rationality community" makes its members' pronouncements automatically feel a little like argument from authority, even if they don't intend them as such.
A lot of people bristle at the notion that anyone is telling them what to think, especially on philosophical matters (which many people think they can figure out for themselves). "Hey," the listener thinks, "I'm not part of your community, but I'm rational too, dammit!" Indeed, this is true - there are plenty of people who try very hard to think rationally, but have never even been to LessWrong.
Also, lots of people just aren't interested in A.I. risk, or effective altruism, or the other stuff people in the "rationality community" like to talk about. They might resent the implication that in order to be a "rational" person you have to care about these things.
Ironically, I'm not sure if the "rationality community" even gave itself that name in the first place, or wants to keep it, which is why I put it in quotes. Anyway, anger at a name seems to plague a lot of communities and movements, either unfairly (Black Lives Matter), fairly (the pro-life movement), or just plain ludicrously (the "reality-based community").
2. The "leaders"
For whatever reason, humans tend to look at any movement or community and pick out some individuals who seem to be the leaders. In the case of the "rationality community", those leaders are generally perceived as being Eliezer Yudkowsky, Scott Alexander, Julia Galef, and Robin Hanson. This is through no fault of their own - they never claimed leadership as far as I know. But human perception is what it is.
Every individual rubs some people the wrong way (except Noah Smith, obviously, who is beloved by all!). Yudkowsky probably strikes some people as a dreamer obsessed with sci-fi. Alexander has clashed with a number of Social Justice people, and generally tends to be a detractor of feminism. Hanson has on occasion gone out of his way to say things he knew would offend people. (I doubt Galef has pissed anyone off.)
So there is probably some personality-friction with these "leaders" of the community. Also, smart people tend to be a contentious bunch, not without their own egos.
3. The fans
Every community and every thinker has fans eager to go to bat for them in online arguments. I'm sure there are some Noahpinion fanbois and fangurlz out there waiting to pounce on my detractors. Anyway, these fans tend not to be a representative random sample of the population - Krugman fans will tend to be liberal, Rod Dreher fans will tend to be conservative Catholics, etc. "Rationality community" fans tend to be libertarian types, in my experience, and especially techno-libertarian types.
I like techno-libertarians (I live in Silicon Valley, don't I?). But not everyone does. Epithets like "techbro" and "brogrammer" are relatively common, They do tend to be men, I guess, though I've met about as many female LessWrong readers as male. Anyway, American society is an especially divided one, and dislike of the social groups from which the "rationality community" tends to be drawn will naturally predispose some people negatively toward the community.
Also, online interactions tend to be negative, contentious ones, meaning that people outside the "rationality community" will tend to have fights with its members. I can remember a time when I got into an argument with (I think?) Eliezer on Twitter, and I made some joke, and some LessWrong dude jumped in and yelled "Monkey dominance tactic!" at me. It made me laugh, because that was such a monkey dominance tactic. But if I were more prone to group attribution error, I would have thought "Fer chrissake, those LessWrongers are annoying!". Kind of like when someone cuts you off in traffic and you look to see what race and gender they are before deciding who to hate. ;-)
Anyway, those are my hypotheses for why a seemingly innocuous online community mostly populated by shoegazing nerds might annoy some people out there. It certainly doesn't annoy me, though.