Back in the second century when this practice began, it was common to honor a ruler with a gesture of respect. Whether bowing down on one knee or touching the forehead, such gestures were ritual ways to show humility before a person of great power.
The Sign of the Cross became one such devotion to the Holy Trinity, and acted as a sign of recognition between early Christians who were sometimes forced to worship in secret.
Now a prayer in itself, each time we make the Sign of the Cross we express respect for God and call down his blessings on ourselves.