Lightly spray a 9×13 inch glass baking dish with nonstick cooking spray. Set aside.
In a large frying pan, heat the olive oil and sauté the peppers and onion.
Lay a tortilla flat on a plate. Spread 1/8 cup of the beans on the tortillas. Scoop about ⅓ cup of the vegetable mixture on top of the beans; sprinkle with cheese. Roll up tightly and place the burritos seam side down in the baking dish. Repeat with the rest of the tortillas.
In a separate bowl, whisk together the eggs, milk, flour, salt, and pepper. Pour the egg mixture over the tortillas; sprinkle with remaining cheese. Cover the dish with foil and refrigerate overnight.
In the morning, preheat the oven to 350 degrees. Bake (with foil on), for 40 minutes. Remove the foil; bake for 20 minutes more, until the cheese is melted, and the eggs are set. The burritos will be golden on top.
Garnish with chopped tomatoes, avocados, cilantro, or salsa.