The ransom amount is minute compared to the value of the goods on board. It's gotten to the point where it's a regular business. You don't expect or assume they will start randomly gunning people down. Just pay the money and get the hell outta there.

I also assume the pirates sort of know what they are looking for. It's pretty obvious which ships are armed navies and which aren't. Private companies aren't allowed to level a city unless the management want to be dragged down to the Hague for some 'splaining.

And any cargo that is worth defending (nuclear, weapons, etc.) can hire mercenaries like Blackwater.