The problem is who controls them. The government of each country can decide at any moment that they want to take control of their TLD and remove any sites that they don't like. It's just not good practice if you want your site to stick around.
Right. So how do you differentiate between the 2-letters ones and 3+? Each TLD can have domains requisitiioned by a government, even if its indirect through ICANN.
ICANN is certainly not perfect, but there is a difference between the automatic control that countries have over their ccTLD and the control they have through ICANN.
The US regularly seize domains, even those with foreign registrars. I don't feel that any tld is immune from this. Sure there are some TLDs more at risk than others, like .af being in control of the Taliban, but I'd also say US controlled TLDs are not the least at risk.