The six-pointed star has long been associated with the Jewish People. In Southern Italy, a tombstone dating back to 300 C.E. was found with a six-pointed star on it. In the year 1354, King Carl IV insisted that the Jews of Prague make a flag for themselves that would feature the six-pointed star as well as the five-pointed star of King Solomon.
The words "Magen David" literally mean "Shield of [King] David." Some say that the soldiers of King David's army wielded shields in the shape of a six-pointed star. King David's personal royal seal, however, was not a star, but rather a shepherd's staff and bag. His son, King Solomon, used a five-pointed star for his personal seal.
In Kabbalistic teachings, one finds that the number six represents the Heavens and the Earth and the four directions (North, South, East, West). There are those who suggest that the Magen David with its six points correspond to this Kabbalistic idea, which in turn can represent God's Omnipresence.
An interesting footnote: the words "Magen David" in Hebrew - מגן דוד - are made up of six letters.
