The basic rationale for quarantine (which for the purpose of this article I'll define to exclude voluntary isolation) is that they reduce the number of infections. But there are several excellent reasons to oppose quarantines, and during COVID-19 is the prime time for me to write about them. First, the moral arguments.

They are an act of aggression.

Any honest philosopher will come to the conclusion that involuntary interference with someone else's autonomy is a prima facie I hate to use that phrase because it makes me sound like an academic "philosopher", but I can't find an adequate substitute wrong, and that this doesn't stop mattering in the face of a dire situation, even if the consequences can outweigh it.

Some bad faith bootlickers on Twitter or other internet comments will argue that this point is moot because if a person was going to voluntarily self-isolate, well then they shouldn't have a problem with being quarantined because it's not actually against their will. I find it very difficult to read this as sincere but I'll deal with it just incase: isolation only requires that you don't go into contact with others, not that you stay inside an arbitrary particular space designated by the 'authorities'. A quarantine is massively more restrictive than the safety of others requires.

With this understood every argument for quarantines must depend entirely on the thought that you can't trust strangers to not go infect others if you don't quarantine them. It is inherently an argument for preemptive violence against someone for possibly having destructive intentions, without any evidence of such. (The analogy between quarantines and gun confiscation is incredibly strong; libertarians who support quarantines are massive hypocrites.)

Quarantines involve the enforcement fallacy.

Distinct from the resource cost of enforcement (see below), in any quarantine of substantial size and duration, there will be people who try to escape it, and guards will be faced with shoot or allow. Justifying involuntary detention is one thing, but justifying murder is entirely another.

Now some more pragmatic arguments.

Quarantines carry massive danger of infecting people who were not yet infected by forcing them into proximity with those who are. This should not be underestimated.

This doesn't apply to quarantines that only imprison people known definitely to be infected, but that isn't how it's being done.

COVID-19 is far less deadly than many seem to think.

I make a point it to call it COVID-19 and not 'coronavirus', becuase 'coronavirus' technically encompasses a lot more than the current COVID-19 outbreak.

Yes, this point isn't relevant to the concept in general, but in the context it's being talked about, the media is really overhyping the danger. COVID-19 is almost never lethal, and most of the people who do die had preexisting conditions; in fact the symptoms are usually not that much worse than a common cold or flu (albeit it depends heavily on your age). Most who catch it recover without medical care in a matter of weeks. Some people have caught it and recovered in a matter of days (to be fair, it's possible reading that story that he didn't actually have COVID-19, but his symptom descriptions match).

It's obvious that the reason the media is overhyping the danger is because they are state shills who all want the state to have more power. In the eloquent words of Nullus Maximus, the corporate press is the enemy of the people. As much as I hate quoting that asshole, it's just a really good slogan.

The power will be used as a political weapon.

This doesn't concern the abstract concept of a quarantine, but in the present world only states have the power to enforce quarantines, and wanting them of all people to have this power is moronic. States that can get away with taking more of people's freedom will certainly use that as a weapon against those they despise. Similar things happened to Japanese Americans during WW2; states will do that again when they have a motivation to.

Quarantines require costly enforcement.

A talking point I also raise about prisons, borders, and lots of other things. It's a good talking point. Resource costs of an action aren't everything, so I list it last, but they absolutely matter.