Bring a large pot of lightly salted water to a boil. Add pasta and cook until tender yet firm to the bite, 8 to 10 minutes.
While the pasta is cooking, melt butter with olive oil in a skillet over medium heat. Add shallot, garlic, and habanero pepper; cook and stir until lightly browned and fragrant, about 2 minutes. Remove from the heat.
Bring cream to a simmer in a saucepan over medium heat. Stir in shallot mixture and tomato, then mix in flour and black pepper. Simmer until thickened, 5 to 8 minutes. Stir in Parmesan cheese. Remove from the heat and let sit until pasta is finished.
Drain pasta. Serve pasta on plates and ladle sauce over top.