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 seal 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. Interestingly, the words "Magen David," in Hebrew, are made up of six letters.
Some people have the tradition of hanging a Magen David in their Sukka. Perhaps the six sides allude to the six "Ushpizen" guests who visit during the first six days of Sukkot: Avraham, Yitzchak, Ya'akov, Moshe, Aharon, and Yosef. The star as a unified whole symbolizes the seventh "Ushpizen" - David - the "king" who unifies the whole. Furthermore, the Magen David has 12 sides: David as king unified the 12 tribes.