This quote is often shortened/paraphrased to a condensed version: "Those who would trade liberty for safety deserve neither."
In an American context, Franklin's line plays on the idea that liberty is the thing we would be protecting by choosing safety. In opting to give up liberty in favor of safety, we are essentially gaining nothing.
The thing we value most (liberty) is lost if we elevate safety to a place of primary value. The essence of this idea, to me, is that liberty entails some necessary degree of uncertainty. Liberty stands in opposition to tyranny, to paranoia and to knee-jerk militarism.
When people have liberty (freedom of choice, freedom of speech, freedom of action, freedom of movement, etc.), they are not being controlled and so might go "out of control" and use that liberty to harm others. If a position was adopted that sought to curb liberty so that people would or could not go "out of control" then people would effectively be controlled. In opting for safety of this kind, freedom of movement, freedom of choice, freedom of speech and freedom of action would be reduced or eliminated.
Thus, in choosing safety over liberty one is choosing safety instead of liberty.