Add the pancetta to a heavy large skillet over medium heat. Add olive oil and saute until golden brown, about 8 minutes. Add the onion and saute until tender, about 5 minutes. Season with salt. Add the garlic and red pepper flakes. Saute until fragrant, about 30 seconds. Stir in the tomato puree. Simmer uncovered over medium-low heat until the sauce thickens slightly and the flavors blend, about 15 minutes. Season the sauce with salt, to taste.
Meanwhile, boil the linguine in a large pot of boiling salted water until tender but still firm to the bite, stirring occasionally, about 8 minutes. Drain, reserving 1 cup of the cooking liquid.
Toss the linguine with the sauce in the skillet, adding some of the reserved cooking liquid until the pasta is moist but being careful not to dilute the sauce. Toss with the cheese. Season with salt, to taste.