Brown the ground beef and onion in olive oil in a large skillet. Add the garlic, basil, pepper flakes and salt to the skillet and stir until fragrant (about 1 minute). Add 2 1/4 cups of water, the tomatoes with juice, and the dried pasta. Bring to a boil; cover and lower temp to a simmer. Cook for 15-17 minutes or until the pasta is tender, stirring occasionally.
Combine the remaining 1/4 cup water and the flour; stir into the mixture in the skillet. Bring the mixture to a boil; cook until thick. Remove from the heat.
Stir in the cottage cheese and half and half. Sprinkle with grated Parmesan cheese before serving.