The situations are hardly comparable. The original poster is talking about giving people the option to isolate themselves in situations where it is not socially acceptable today, quarantine tends to mean forced separation. This is very important qualitative difference.

Something funny is going on with people's moral reasoning here

Based on my general experience, I would say that most people engage in what I would call "Miss America Moral Reasoning," i.e. their main priority is to figure out what position will be most impressive to the (perceived) judges.

Do rationalists and/or wannabe rationalists behave in this way? Probably a lot do, but it's rather hard to assess.

Re magnitude-dependent utilitarian contradiction: Perhaps the difference is the number of cases. If you only limit the freedom of only a couple of poeple (those who suffer from rare diseases) the risk of stigmata and exclusion seems intuitively high. In the other case it would be more of an collective effort, because pretty much everyone has to deal with colds on a regular basis.

My guess on why this is well-received is that the immediately obvious consequences are positive. You don't have to go to work and you're allowed to reschedule flights when you're sick. Most people have had to work while sick, which is miserable, and a lot of people have been sick on trips, which pretty much ruins them. I don't think the reasoning extends much beyond that.

But when you talk about indefinitely quarantining people with incurable diseases, that feels like persecution of a minority group for something outside of their control, which everyone knows is Bad™.

Also, the phrasing of the quoted comment doesn't sound like a mandate.

...why not also require people to be able to reschedule flights if a doctor certifies they have a contagious disease?

I predict you'd get a different response if the proposition was to forbid people from flying while showing any symptoms of being sick and fining people for sneezing on an airplane.

Well I wasn't proposing a strict quarantine or limits on travel. Merely preventing people from coming into close contact with colleagues at work where the risk of contagion is highest, and requiring them to have the option to reschedule their (expensive) travel. People are already familiar and comfortable with regulations in workplaces and aviation.

If I were proposing a thoroughgoing quarantine, I expect people wouldn't be nearly as enthusiastic.

When someone has an incurable and lethal respiratory illness, I think we do require them to stay in quarantine and this is broadly accepted. The reason this doesn't apply to HIV and other such diseases is that they are barely contagious.

Related to what James Miller said, it seems analogous to the experimental finding that white American liberals are more likely to sacrifice whites (relative to blacks, at least) in the famous trolley thought experiment.

Something funny is going on with people's moral reasoning here and I suspect it isn't peculiar to rationalists, but reflective of something in wider culture.

Maybe it is peculiar to rationalists, or I should say, "rationalists": people who think they're rationalists. Quarantining people with colds and not quarantining people returning from places with Ebola have this in common: it is the opposite of the practice seen in the wider world. Therefore, if you take this view, and assemble clever arguments for it, you must be being more rational.

The argument is quite well received by the very reasonable facebook rationalists crowd. However many rationalists were quite clearly squicked out by the idea of quarantine when applied to lethal diseases ( http://lesswrong.com/lw/l3u/link_the_coming_plague/ ), yet talking about the minor inconvenience of colds suddenly everyone is a utilitarian and is willing to suspend certain supposedly sacred rights.

Are you sure the same individuals are doing those? Muhammad Wang fallacy, and all that.

As I'm sure you have considered, issues relating to racism and homophobia come into play.

You have left out another difference: whether the person is known to be infected.

Many people reserve the word "quarantine" for those exposed, but not known to be infected; and use "isolation" for those exhibiting symptoms. They are expected to appreciate the medical care, although that is not relevant in the case of the common cold. No one has objected to the isolation of people exhibiting symptoms of Ebola after exposure.

The response to SARS quarantines seemed to me pretty similar to the response to Ebola quarantines.