At least one .org website that I know of has been shut down because the USA pressured the US organisation that controls the .org domain into doing so.
They could repeat this at will for quite a number of sites.
An immediate step to prevent this possibility, if you run a website, is to register a domain that is controled outside the US.
I have not found one article that just lists them all, and who controls them, but most TLDs have their own wikipedia article, e.g. .org (US controled), .eu (not US controled, yay) etc.
Ultimately ICANN controls all of this, and that's a US orga too, and Trump could bully them into doing shit, too. But the people who know about these things don't seem to think that's a likely threat right now. Also ICANN seems to defer a lot of tasks to exactly these TLD orgas. After all the internet still is (somewhat) decentralized.
Not to defend this bullshit action (by the US government) in any way, but it seems like panic might be premature - whereas caution is always a good idea.
As far as I can tell, this bullshit reason about "antifa" (which is US fascism bullshit¹) is, so far, unprecedented. This is the first time.
Is this the last time? Sure, that seems unlikely.
And again, I emphasize that I think caution is advised.
So sure, if you're starting up an organization or otherwise running one that might piss of the fascists, making sure you're running it on a TLD (or ccTLD) that is not controlled by a US organization is not a bad idea.
But if you're making those sorts of plans, definitely look at other ways of communication that also don't rely on US-controlled orgs, because as pointed out, ICANN is a US org, so if they can put pressure on a registrar, they can put pressure on ICANN for sure.
¹ as opposed to "terrorism", which is at least debatable and probably often valid and only somewhat abused