Flying bombs preferred target is buildings.Bunkers only reduce damage done by units.
A lvl 1 bunker was not strong enough to take the damage and protect your infantry against your flying bombs.
The amphibious tanks are not buildings and took little damage and therefore survived and captured the city.That's my guess.
Flying bombs are not really sufficient against units.I had to use 7 flying bombs to take out a 3 stack of 1 AC and 2 infantry all lvl 1's.