Preheat oven to 350°F (175°C). Grease a 9x13-inch baking dish.
Bring a large pot of lightly salted water to a boil. Add ziti pasta and cook for 8 minutes or until al dente; drain.
In a large skillet over medium heat, cook the ground beef, onion, and garlic until the beef is browned. Drain off any excess fat.
Stir in tomato sauce, Italian seasoning, red pepper flakes, salt and pepper. Simmer for 10 minutes.
In a medium bowl mix together the ricotta cheese and 1 cup of mozzarella cheese.
Spread 1/2 cup of the meat sauce in the bottom of the prepared baking dish. Layer with half of the cooked ziti noodles, all of the ricotta mixture and 1/2 cup meat sauce. Top with remaining ziti noodles and meat sauce.
Cover with remaining 1 1/2 cups mozzarella cheese.
Bake in preheated oven for 30 minutes or until cheese is melted and bubbly.