Probability of dying in a plane crash is 3*10^-7 (source). At hundred dead passengers a flight, fatal crashes are ~ 10^-5. Off by two orders of magnitude.

If there are 3*10^6 flights in a year, and one randomly selected plane crashes per year on average, with all aboard being killed, then the chances of dying in an airplane crash are , surely?

Yes, there's a hundred dead passengers on the flight that went down, but there's also a hundred living passengers on every flight that didn't go down. The hundreds cancel out.