Cook the penne pasta according to package instructions in a large pot of salted boiling water until al dente. Drain and set aside, reserving 1/2 cup of the pasta water.
In a large skillet, heat the olive oil and butter over medium heat. Add the chopped onion and sauté until translucent, about 5 minutes.
Stir in the minced garlic and red pepper flakes, cooking for another minute until fragrant.
Add the crushed tomatoes to the skillet, stirring to combine. Simmer for about 5 minutes, allowing the sauce to thicken slightly.
Reduce the heat to low and stir in the heavy cream, mixing well. Gradually add the grated Parmesan cheese, stirring until melted and smooth.
Season the sauce with salt and black pepper to taste. If the sauce is too thick, add some reserved pasta water until the desired consistency is reached.
Toss the cooked penne pasta in the sauce until well coated. Cook for an additional 2-3 minutes to heat through.
Serve immediately, garnished with fresh basil leaves and extra Parmesan cheese if desired.