Melt the butter with olive oil in a medium skillet. Add the chopped onion, cook over medium heat until the onion is soft and translucent, about 5 to 6 minutes. Add the garlic and cook stirring for 15 more seconds. Then pour in the crushed tomatoes and bring to a simmer - season to taste with chili flakes and salt. Simmer for 15 minutes.
Meanwhile, bring a medium pan of salted water to a boil. Cook the penne until al dente about 10 to 11 minutes, or according to package instructions. Drain the pasta and save 1/4 cups of cooking liquid.
Add the pasta along with the cooking liquid to the tomato sauce stir well to coat and cook together for 1 more minute to merge the flavors.
Adjust the seasoning to taste and serve right away.