Flasher just controls on/off of the circuit; it's the actual turn signal switch that controls the individual lights.
Rear turn signals are on the same side of the bulb/socket as the brake lights...which are NOT connected to the front turn signals. So current from the brake light switch also goes through the turn signal switch...but the position of the switch determines which one stays on when your brakes are on, and which one flashes. So there are separate "output" wires from the turn signal switch for left front, right front, left rear, and right rear.
Think about it for a second. It'll make sense to you. Check out the diagrams at the link below; they may help you understand how it all works.