Between the eyes is usually used figuratively to say that a plan was executed perfectly. "I got him between the eyes" is similar in meaning to "I dealt a knockout blow". In the example it is literal, a rock was thrown and hit the person in the middle of the forehead.

Between means you have something on the left and other on the right. between the eyes you have the nose haha "The middle of the face" and "between the eyes" are almost the same thing