When you overthrow a ruler or a regime, you throw them out, usually by force. If you're a rebel you may plan to overthrow the current government and install a new regime.
You can also use overthrow as a noun. You might plot to overthrow the parking ticket authority so that you won't have to pay your tickets. There are also more literal uses of the word. In baseball, football, and other games that involve throwing a ball, you overthrow when you throw the ball past the person you're aiming for. You can say "the pitcher overthrew the ball to the first baseman," or "the pitcher overthrew the first baseman."