In a large Dutch oven, cook the onions in the oil over medium-high heat, stirring often, until the onions have softened but have not taken on any color, about 10 to 12 minutes.
Add the garlic and red pepper flakes and cook for 2 additional minutes.
Add the wine and cook until it is almost fully evaporated, about 2 minutes more.
Add the tomatoes, calamari and pepper and bring to a boil.
Reduce to a simmer and cook, stirring often, until the calamari is tender, about 1 hour.
Season with salt, to taste.
Serve with linguine and garnish with chopped parsley.