Prepare pasta according to package directions; drain and rinse under cold water and set aside. Preheat oven to 375°.
In a medium saucepan, melt margarine over low heat. Stir in flour with a whisk and cook, stirring, for 1 minute. Gradually whisk in the milk and bring the sauce to a boil, stirring constantly. Remove from heat and add Cheddar cheese, cayenne pepper and salt. Stir until the cheese has melted.
In a large mixing bowl, stir the cheese sauce and pasta together. Spoon into a 1 1/2-quart oven proof casserole dish. Sprinkle Parmesan cheese over the top. Bake until browned on top and hot all the way through, about 30-35 minutes.