Bring a large pot of water to boil for the pasta. Add 1 tablespoon of salt to the water once it's boiling (this is your only chance to season the pasta itself).
Heat olive oil in a large skillet over medium heat until shimmering. Add diced onions and cook for 4-5 minutes until they become translucent.
Add minced garlic and cook for another 30 seconds until fragrant, being careful not to burn it as this will create bitterness.
Increase heat to medium-high and add ground beef to the pan. Break it apart with a wooden spoon and cook until no pink remains, about 5-7 minutes. Drain excess fat if necessary.
Stir in tomato paste and cook for 1-2 minutes to caramelize slightly, which deepens the flavor of your sauce.
Add crushed tomatoes, tomato sauce, dried herbs, red pepper flakes, and sugar. Stir well to combine. Reduce heat to medium-low and allow to simmer for at least 15 minutes, stirring occasionally.
While sauce simmers, cook linguine according to package directions until al dente, usually 9-11 minutes. Reserve 1/2 cup of pasta water before draining.
Drain pasta but do not rinse. The starch on the surface helps the sauce adhere better.
Add drained pasta directly to the sauce along with 1/4 cup of the reserved pasta water. Toss until pasta is evenly coated, adding more pasta water if needed to achieve desired consistency.
Stir in 1/2 cup Parmesan cheese until melted. Taste and adjust seasoning with salt and pepper as needed.
Serve immediately in warm bowls, garnished with additional Parmesan and fresh herbs if desired.