catholic theology takes it as being mary. you see it in much of the artwork; mary stand on the moon with a crown of 12 stars. Even the EU flag is based on the crown of Mary - 12 gold stars. (the only reference to christianity in the EU, thanks to a good ole catholic monarchist Otto von Hapsburg)
“She gave birth to a son, a male child, destined to rule all the nations with an iron rod. 5 Her child was caught up to God and his throne. “ rev. 12:5
Found this on Wikipedia, for what it's worth.
The flag was originally adopted by the Council of Europe on December 8, 1955, from one of many designs attributed to Arsène Heitz[1]. On 25 October 1955 the Parliamentary Assembly made the unanimous decision to adopt a circle of gold stars on a blue background as an emblem. On 8 December 1955 the Committee of Ministers adopted this as the European flag. "Against the blue sky of the Western world, the stars represent the peoples of Europe in a circle, a symbol of unity. Their number shall be invariably set at twelve, the symbol of completeness and perfection...[So far so good.]
...just like the twelve signs of the zodiac represent the whole universe,
[Ruh-roh.]
...the twelve gold stars stand for all peoples of Europe – including those who cannot as yet take part in building up Europe in unity and peace."