Heat oil in a Dutch oven or large heavy skillet, over medium heat.
Add guanciale and sauté until crisp and golden, about 4 minutes.
Add pepper flakes and black pepper; stir for 10 seconds.
Add onion and garlic; cook, stirring often, until soft, about 8 minutes.
Add tomatoes, reduce heat to low, and cook, stirring occasionally, until sauce thickens, 15 - 20 minutes.
Meanwhile, bring a large pot of water to a boil; season with salt; add the pasta and cook, stirring occasionally, until 2 minutes before al dente; drain, reserving 1 cup of pasta cooking water.
Add drained pasta to sauce in skillet and toss vigorously with tongs to coat.
Add 1/2 cup of the reserved pasta water and cook until sauce coats pasta and pasta is al dente, about 2 minutes; add a little pasta water if sauce is too dry.
Stir in cheese and transfer pasta to warmed bowls.