We did charter flights to fly our citizens home. And we still charter flights to fly our citizens home.
Ever since the outbreak in Melbourne, we have capped those flights at 4,000 people per week. (They were initially capped at 7,000 people per week.)
The reason that we have done this is due to our hotel quarantine system. We need to bring home the quantity of people we can safely quarantine, without stressing the systems too much.
The quarantined people need to be bused, housed, then watched (obviously, after Melbourne), fed, tested twice per person, and people need to run around and get them everything they want.
Almost none of these returning citizens are coming from a 'safe' country. They are coming from countries that are loaded up with the virus.
As was stated in a previous post, flights were flying freely until the end of March when the initial capping went into place. My US visitor flew back to the US in June on one of the in/out charter flights.
Australians were warned and warned and warned that the borders were closing and coming home would grow more difficult. (As was my US visitor, in regular emails from the US embassy.)
'I'm screwed': Australians fear being stranded overseas after inbound flights slashed