There is always some degree of controversy surrounding exactally how the BCS determins which two teams will play in said game. But it seems to have a lot to do with popularity, and the amount of money that can be made off of the game.
It has almost nothing to do with how good your team really is. Especially if your team is from a smaller, non big-money school. as you will seemingly never get a chance to play in it. They will even use the officals to thier favor in altering games that would force them to give you a shot, instead of the team they want to go.