They are the religious eras. The way that we get the city art and music to switch when you change religions (we change to a era specific to that religion). But it doesnt make any sense to start the game in the Runes era, etc.
The only real change from selecting those eras is that you will start with all the techs (since they are in the era file after the rennisaunce era) and you city art and music will be from whatever religion your era is supposed to match.