As most commercial aircraft cruise at an altitude of between 36-40000ft, then the chances of being shot by a bullet fired from the surface (land/sea) is very, very unlikely.
Shot down by a military aircraft(Air to Air missile/cannon)? Possible, but unlikely.
Shot down by a missile (surface to Air)? Again possible, but who and why?
The chances of any of the above happening, and the aircraft surviving intact enough to make a controlled landing on the sea without breaking up on impact? Infinitesimally small.
Lack of radio comm's suggest either hijack, or catastrophic failure of the avionics/comm's systems/navigation systems. The aircraft was tracked on both primary and secondary radar for a period, then via it's Inmarsat signal for a number of hours after radar contact was lost, up to the point it potentially ran out of fuel. It is certainly possible that the aircraft could have been secretly diverted somewhere, but it would take months if not years to plan something this audacious, and again, you have to question the motives.