Is this different than the DoD having a root certificate in iOS (and I think Windows, too)? Couldn't the DoD also MITM the traffic any time they wish?
At a basic level, yes, any CA can issue a certificate which can be used to launch a MITM attack. We trust that the CAs don't do this. If they're caught, the browser industry tends to revoke their CA status -- which is pretty bad for the CA's business model.
That said, the CAs have been under increased scrutiny lately, and browsers are starting to build additional protections against this kind of thing:
- Certificate pinning (HPKP) allows sites to restrict which certificates can be used for a specific host, even if the certificate is signed by a trusted system root. (Caveat: HPKP isn't enforced for local roots, installed by an admin. That's how Kazakhstan is able to get away with this, because they're asking users to install a new root manually.)
- Certificate Transparency is supposed to provide an audit log for CAs, so that any maliciously issued certificates can be detected and acted on.
That said, these features are new and not universally supported by all browsers. And neither would help in a case like Kazakhstan, where users are being asked to bypass security features and there's no system root to revoke.