Heat the 2 tablespoons of olive oil in a large (at least 4 1/2 quart) stock pot or Dutch oven over medium heat. Add the pound of Italian sausage and the diced onion, and cook until sausage has browned, about 10 minutes, making sure to crumble the sausage as it cooks. Stir in the 3 cups water, 1 1/2 pounds chopped tomatoes, 1 pound pasta, 2 cups basil leaves, 4 sprigs fresh thyme, 2 cloves of chopped garlic, 1 sprig rosemary, and 1 teaspoon kosher salt.
Bring to a boil; reduce heat and simmer, covered, stirring occasionally, until pasta is cooked through, about 9-12 minutes. This will depend on the type of pasta you use. Start testing pasta at 9 minutes.
Remove the thyme and rosemary sprigs, taste and season with more salt if needed. Serve topped with parmesan cheese and red chile flakes.