Fatalities per trip is similarly misleading because of the number of extremely short trips people make in cars.
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.