When comparing a difference of 1000x, sure its probably safer.
Your premise is wrong though, it isn't common sense to take a generalized statistic like deaths per km and extrapolate that to be the correct estimate for any particular trip.
The statistic loses all context of differences in vehicles, road conditions, time of day, specific roads, etc. The stat is a great example of how a statistic seems meaningful to get a big picture but is completely useless to us as we can't make any decisions based on a number that is so generalized as to lose all context and meaning.
Assuming that the survival rate is constant as a function of trip length, the empirical estimate of the risk is fully determined by the number of deaths per distance.
Airline travel is much riskier in takeoff and landing phases. A bunch of 200 mile flights is riskier than a 3500 mile trans-con trip.
Car travel is much safer on controlled access highways than 40 mph surface streets.
That's an assumption that doesn't hold up, at least that's the argument I was trying to make above.
Generalizing so much data down to a single statistic makes the number useless. Almost all context is lost, really the only context kept is mode of transportation and distance traveled. That isn't enough to help anyone make a decision for any particular trip.
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.
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 :-) ).