Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente, about 10-12 minutes. Drain and set aside.
While the pasta cooks, heat the olive oil in a large skillet over medium-high heat.
Add the ground beef to the skillet and cook, breaking it apart with a spoon, until browned and cooked through, about 6-8 minutes. Drain excess fat if necessary.
Add the chopped onion to the skillet with the beef and cook until softened, about 3-4 minutes.
Stir in the minced garlic and cook for 1 minute until fragrant.
Pour in the crushed tomatoes, then add the dried oregano, dried basil, salt, black pepper, and red pepper flakes. Stir to combine.
Reduce the heat to medium-low and simmer the sauce for 10 minutes, stirring occasionally.
Add the cooked penne pasta to the skillet and toss well to coat the pasta evenly with the sauce.
Remove from heat and stir in the grated Parmesan cheese.
Garnish with chopped fresh parsley before serving.