Vehicles designated in the various APC/IFV classes protect their passengers under their armour (if any), I believe this is also true of the amphibian class. A soft vehicle, ie one without armour, doesn't protect its passengers.
A sniper, or other unit, firing at a soft vehicle (or through the open top of an open armoured vehicle) needs to kill the crew to "destroy" the vehicle. No one will survive if a passenger in a destroyed vehicle in deep water.
AFAIK the game does NOT handle flamethrowers as any different from other infantry types.
Sounds like your soft skin / opentopped amphibs had their crew killed in open water destroying the vehicle and all occupants - makes no difference if a flame thrower was onboard or not!
Smoke is your friend!
