Heat the oil in a 12-inch skillet over medium-low heat. Add the onion and cook, stirring, until soft, about 12 minutes. Add the garlic and cook, stirring, for 2 to 4 minutes. Add the red pepper flakes; cook for 1 minute more. Increase the heat to medium, add the pureed tomatoes, and season lightly with kosher salt; cook, stirring occasionally, until the sauce thickens slightly and the flavors meld, about 20 minutes. Remove the pan from heat, stir in 3 large fresh basil sprigs, and set aside.
Meanwhile, bring 3 quarts water to a boil in a 5-quart pot. Season with salt; add the pasta and cook, stirring occasionally, until about 2 minutes before tender. Drain the pasta, reserving ½ cup of the pasta cooking water.
Discard the basil and heat the skillet over high heat. Stir in the reserved pasta water to loosen the sauce; bring to a boil. Add the pasta and cook, stirring, until the sauce coats the pasta and the pasta is al dente, about 2 minutes. Remove the pan from heat; add the butter and Parmesan; toss until the cheese melts. Transfer to warm bowls; serve with more cheese, if desired.
Notes
When you puree your tomatoes, give them enough time to get really pureed... otherwise you'll have chunks. You want a nice, smooth sauce.