Preheat oven to 450° F. Fry the bacon until crisp. Remove from skillet, drain and crumble. Discard all but 1 tablespoon of the grease. Reheat the skillet over medium heat. Add the onions and sauté for about 5 minutes; do not brown. Place the beaten eggs in a medium bowl. Beat in the flour, salt and pepper. Add the milk and beat until well blended. Stir in the cheese and bacon. Add the onion and stir. Pour into pie shell. Bake for 10 minutes, then reduce the temperature to 350° and continue baking for about 20 minutes, until a knife blade inserted in the center comes out clean. Remove from oven and let stand for 10 minutes. Cut in wedges; serve warm.