Preheat oven to 375 degrees. Lightly coat a 2 quart shallow baking dish with cooking spray. Heat olive oil over medium heat in large nonstick skillet. Add onion, and cook until softened, but not brown. Add red pepper, and cook just until softened, about 3-5 minutes. Add squash and garlic, and cook, stirring until squash is transparent. Add salt, pepper, and thyme. Stir in tomato, and remove from heat. Transfer ingredients to baking dish.
In a medium bowl, mix together eggs and milk. Add grated cheese, and combine. Pour over sautéed veggies, and bake for 30-40 minutes, or until firm and golden brown. Serve warm, or at room temperatures. 2 large servings.