Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente. Drain and set aside.
In a large skillet, heat the olive oil 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 an additional 1-2 minutes until fragrant.
Pour in the crushed tomatoes, oregano, and basil. Season with salt and pepper to taste. Bring the sauce to a simmer and let it cook for about 10-15 minutes, stirring occasionally.
Add the cooked penne to the skillet with the sauce, tossing to combine and heat through for about 2-3 minutes.
Serve hot, garnished with fresh parsley and grated Parmesan cheese.