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 olive oil in a large skillet over medium heat.
Add the chopped onion and cook until softened and translucent, about 4-5 minutes.
Add the minced garlic and cook for 1 minute until fragrant.
Add the ground beef to the skillet. Cook, breaking it up with a spoon, until browned and cooked through, about 6-8 minutes. Drain excess fat if necessary.
Stir in the crushed tomatoes, tomato paste, dried oregano, dried basil, salt, black pepper, and red pepper flakes.
Reduce heat to low and simmer the sauce for 10 minutes, stirring occasionally.
Add the cooked pasta to the skillet with the sauce. Toss to combine and heat through for 2-3 minutes.
Remove from heat and stir in half of the grated Parmesan cheese.
Divide the pasta among serving plates. Sprinkle with the remaining Parmesan cheese and chopped fresh parsley before serving.