Bring a large pot of lightly salted water to a boil. Add pasta and cook for 8 to 10 minutes or until al dente; drain.

Heat olive oil in a large skillet over medium heat. Saute onion until tender and translucent. Stir in garlic and butter, and saute until garlic is soft and fragrant, about 1 minute. Dissolve flour in milk, then stir in. Season with salt and pepper, and simmer 4 minutes, stirring constantly. Add cheese, and stir until melted. Stir in pesto. Add shrimp or chicken, mushrooms and tomatoes. Cook 10 minutes, or until heated through.

Toss with pasta until evenly coated.