If you really start including risk factors you'll never stop, the risk is proportional to many other factors as well:
1) Time of day: Time of day factors in probably for both flying and driving at varying degrees
2) Where: In the US, which state you're driving in matters significantly for driving fatality rates
3) Day of week: Driving on weekends is more dangerous than driving during the week, doesn't seem to affect flights
4) ATC is a variable for flight accidents but not drivers
5) Flights might actually carry more risk per mile in certain situations: Flying over the oceans, eg
A truly correct apples-to-apples comparison would be so hyper-specific as to be useless.
Yet I suspect the people in twin towers weren't included in airline death stats.
Sure there isn't a perfect single metric - just pointing out that the one the airlines prefer appears to be biased towards air-travel.
The other factor that is often ignored is the issue of control. As a passenger of an airline you have very little impact on the chance of an accident - you are just an accident statistic.
Whereas if you are driving, your own driving behaviour, choice of car, route etc puts you more in control of the chances ( though of course by no means completely ).
This has a big impact on the perception of risk ( as more than average think they are better than average :-) ).
So for example with flights - I'd imagine the most dangerous parts are the take-off and landing - which happen once per trip no matter how long you fly for inbetween.
So for flights incidents / kilometer are perhaps misleading.