In a saucepan cook onion and garlic in hot margarine until tender. Stir in flour and pepper. Add milk all at once. Cook and stir over medium heat until thickened and bubbly. Cook and stir for 1 minute more. Add cheese; stir until melted. Stir in drained beans and chili peppers; heat through.
Meanwhile, cook linguine for 8 to 10 minutes or until tender but still firm. Drain well. Serve the sauce over linguine.