I have believed for a long time (although I can't remember how I arrived at this belief) that "to flounder" meant "to flop around like a flounder" i.e. like a caught fish on the bottom of a boat, and therefore meant "to expend a lot of energy in a probably futile struggle." That might be an accurate description of what a boat (or its crew) does in a hurricane.

At any rate, I'm not sure that everyone who says "flounder" means to say, or ought to say, "founder." In fact, it seems to me there are times when "flounder" would be appropriate but "founder" would not.