That would make small countries look unfairly safer because of their shorter flights. Maybe deaths per passenger-kilometer? Unless the duration of the flight doesn't really affect the risk.
Edit: Data to back it up: http://www.1001crash.com/index-page-statistique-lg-2-numpage...
But if all you're looking at is the risk per flight like this, it's like you said, takeoff and landing are where crashes happen regardless of distance.
It's very difficult to compare miles traveled. Even when comparing a cross country trip, how safe am I driving if I come anywhere close to US airline's safety standards: very well maintained car, never drive tired, avoid bad road conditions, etc...?