The goal in prostate examination is to be able to palpate (feel) the entire gland in order to assess its size, shape and detect any irregularities. The gland is shaped somewhat like a triangle with the base at the top and the apex pointing down. Sometimes the base is quite a ways from the opening of the anus, so we use the finger that has the longest reach.
Both the middle and ring fingers have a digit on either side that limits our ability to place them very far in. The three contenders, therefore, are the little finger, index finger and thumb – and the index finger is the longest among those three.