I agree, a random missile hit would be rare indeed. But since I witnessed a "near miss" several years ago over the Grand Canyon area, commercial flying can still give me the willies, even given the enormous statistical safety boons.
How near was it? It buffeted our plane (Southwest Airlines, Phoenix to Sacramento), when another jet airliner flew directly underneath in a near t-bone (west to east) angle. Only myself and one other passenger, who was also window gazing, even saw the other plane streak by. All the other passengers, including at least one flight attendant I talked to, just assumed we had hit a pocket of air turbulence. Scary...that cross-path (west to east) plane looked bigger'n Dallas approaching in the portside window.