Preheat the oven to 375°F. Spray a 9×13-inch baking dish with nonstick cooking spray.
Bring a large pot of salted water to a boil. Cook the rigatoni to al dente according to package directions. Drain and set aside.
Heat olive oil in a large skillet over medium-high heat. Add the ground beef and cook until browned, breaking it apart as it cooks. Drain any excess grease.
Add the diced onion to the skillet and cook for three to four minutes, until softened.
Add the minced garlic and cook for one minute more.
Stir in the tomato paste and cook for one to two minutes.
Add the marinara sauce, crushed tomatoes, Italian seasoning, dried basil, dried oregano, paprika, salt, black pepper, and red pepper flakes if using. Stir well.
Reduce the heat to medium-low and simmer the sauce for 8 to 10 minutes, stirring occasionally.
Stir in the heavy cream and grated parmesan cheese. Let the sauce warm for two minutes.
Add the cooked rigatoni to a large mixing bowl. Pour the beef sauce over the pasta and stir gently to coat.
Stir in one cup of shredded mozzarella cheese and ½ cup of shredded cheddar cheese.
Transfer the pasta mixture to the prepared baking dish.
Sprinkle the remaining one cup of mozzarella cheese and remaining ½ cup of cheddar cheese over the top.
Bake uncovered for 20 to 25 minutes, until the cheese is melted and the sauce is bubbling.
Let the pasta rest for five minutes before serving. Garnish with chopped parsley if desired.