Place the chopped bacon and onion in a skillet over medium heat, and cook and stir until the bacon is crisp and the onion is beginning to brown, about 10 minutes. Add garlic and crushed red pepper flakes and cook another 2 - 3 minutes, being careful not to burn the garlic.
While the bacon and onion are cooking, fill a large pot with lightly salted water and bring to a rolling boil over high heat. Once the water is boiling, stir in the penne, and return to a boil. Cook the pasta uncovered, stirring occasionally, until cooked through, but is still firm to the bite, about 11 minutes. Drain pasta, transfer to a large serving bowl, and stir in the olive oil to coat the pasta.
Drain the bacon grease from the skillet, leaving a couple of tablespoons or to taste. Stir the cooked bacon mixture into the pasta, and sprinkle the Parmesan cheese over the pasta. Stir to mix in the cheese, and serve.