Let's examine the hypothesis in terms of relative target risk. It is conceivable for a meteoroid to down an airliner. It takes a fairly large one to survive entry and have enough mass at terminal velocity. It also has to hit a vulnerable spot. The TWA 800 case suggests that such an object would have to had hit the top of the fuselage, directly over the center tank, and had enough energy to penetrate the pressure vessel, the interior overhead, the floor, and possibly some seats.
Most meteors burn up well above airline altitudes.
Most explode well above air-lanes. Any with enough residual energy after the explosion, or which didn't explode until 13,000 feet, would have caused other effects in the region. There would probably be seismological reports. So our theory leaves us with simple a simple kinetic collision of a hot falling space rock and a mostly-aluminum flying machine. Meteorites of various sizes frequently hit the earth's surface.