In a large sauté pan, heat the olive oil over medium-high heat until very hot. Add the sausage to the pan and use a wooden spoon or spatula to break the sausage into small pieces as it browns. Cook the sausage thoroughly, then remove from pan and discard any excess fat, reserving about 1 tablespoon in the pan.
Add the julienned onions to the hot pan and season with salt and a pinch of red pepper flakes, (add more for a spicier sauce). Cover and cook the onions over medium-low heat for about 5 minutes. Remove the lid and stir the onions. Continue to cook until the onions are wilted and starting to brown, another 5-7 minutes. Add the garlic and thyme and cook for 2 minutes until fragrant.
Next, add all of the canned tomatoes to the pan along with the browned sausage, and stir to combine. Gently simmer the sauce on low heat for 25-30 minutes. Taste and adjust seasonings as desired.
If the sauce is watery, continue to simmer for an additional 5-10 minutes until desired consistency is reached. Stir in the cream, adjusting the seasoning and amount of cream to taste.
Stir the butternut squash noodles into the sauce and cook for 3-4 minutes until the noodles are just tender (be careful not to overcook the noodles or they will tend to break into small pieces). Serve immediately topped with freshly shredded parmesan cheese.