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 the pasta has cooked through, but is still firm to the bite, about 11 minutes. Drain well in a colander set in the sink.

Heat the olive oil in a skillet over medium heat. Stir in the garlic and onion; cook and stir until the onion has softened and turned translucent, about 5 minutes. Stir in the tomatoes; simmer until heated through, about 5 minutes more. Add the lemon juice and shrimp. Cook and stir until the shrimp are bright pink on the outside and the meat is no longer transparent in the center, about 5 minutes. Stir in the parsley, then season with salt, pepper, and red pepper flakes. Serve shrimp and sauce over prepared penne pasta. Sprinkle with Parmesan cheese.