Lightly spoon flour into a dry measuring cup; level with a knife. Place flour in a heavy saucepan; gradually add milk, stirring with a whisk until blended. Place over medium heat; cook until thick (about 8 minutes), stirring constantly. Remove from heat; add cheese, stirring until melted. Set aside.
Preheat oven to 350°.
Steam broccoli, covered, 4 minutes. Drain. Combine cheese sauce, broccoli, penne, and next 5 ingredients. Spoon into an 11 x 7-inch baking dish coated with cooking spray. Bake at 350° for 20 minutes or until bubbly.