Preheat oven to 350°F. Lightly coat twelve 2 1/2-inch muffin cups with nonstick cooking spray; set aside.
Lightly coat a large skillet with cooking spray. Heat over medium heat. Beat together eggs, milk, and salt. Add to skillet. Cook, without stirring, until mixture begins to set on the bottom and around edges. With a spatula, lift and fold the egg mixture so the uncooked portion flows underneath. Cook for 2 to 3 minutes or until egg mixture is cooked through but sill glossy and moist. Remove and set aside.
Use a 4 1/2-inch round cutter to cut 12 rounds from the tortillas. Stack rounds on a plate or in paper towels and microwave for 10 seconds. Use a small drinking glass to press tortilla rounds into prepared muffin cups. Fill with beans, sausage, and eggs; top with cheese. Bake for 15 to 20 minutes or until tortillas are lightly browned and filling is heated through. Remove from cups. Serve with salsa.
Tip: Wrap leftover Burrito Breakfast Cups individually in plastic wrap, place in a plastic storage container or freezer bag and freeze for up to 1 month. To thaw, remove plastic wrap, wrap in a paper towel and microwave on High for 30 to 60 seconds or until heated through.