Bring a large pot of salted water to a boil. Cook the bacon in a large skillet over medium heat until the fat is mostly rendered, about 5 minutes. Discard all but 1 tablespoon of the fat. Add the onion, garlic, and pepper flakes to the pan. Sauté for about 5 minutes, until the onion has begun to lightly brown. Add the tomatoes and season with salt and lots of black pepper. Bring to a simmer. Meanwhile, cook the pasta in the boiling water until al dente (usually about 30 seconds to a minute less than the package instructions recommend). Drain the pasta and add directly to the simmering tomato sauce. Stir together so that the sauce and noodles are evenly incorporated. Stir in the parsley. Divide among four warm pasta bowls, and top with freshly grated cheese.