Preheat a skillet over medium heat.
Add the olive oil to the pan. Add the onion and garlic and sauté while stirring for 2-3 minutes.
Add the tomatoes, parsley, basil, oregano, thyme, red pepper flakes, salt, and pepper. Reduce the heat to low, cover the skillet, and simmer for 30 minutes. For a chunky sauce, simply keep warm until ready to use.
For a Smooth Sauce: Remove the pan from the heat. Puree the sauce with a food strainer, food processor, or immersion blender. Return the sauce to the heat and keep warm until ready to use.
This recipe makes about 5 cups. Store extra in the refrigerator for 2-3 days or freeze for longer storage. Calories based on 1/2 cup serving size.