The relevance of the metric depends on what you're using it for. If you decide whether to drive or fly to a destination based on how safe it is, risk/distance is a perfectly reasonable metric. Since flying is a means of transportation, it seems reasonable to judge the risk relative to the amount of transportation you get out of it.

That doesn't discount the fact that most of the risk is in take-off/landing, so if you use fleet-average statistics you'll bias the risk of short flights low and long flight high. Air safety studies do also use additional metrics like accidents/hour and accidents/segment, but those are mostly useful for comparing between different types of aviation.