Trim fennel bulb, removing any tough outer parts. Slice bulb lengthwise in half and remove core, then cut each half lengthwise into 1/2-inch slices. Separate the slivers of fennel if they are attached at the bottom; cut the long slivers in half.
Bring a large pot of salted water to boil for the pasta. Meanwhile, heat olive oil in large frying pan over medium-high heat. Add sausage meat and cook, stirring and breaking it up with a wooden spoon, for about 1 1/2 minutes, until it sizzles and begins to brown.
Push sausage to side of pan and drop onion slices into the cleared center. Sauté, stirring, for about 2 minutes until onions sizzle and wilt, then mix them into the sausage meat. Clear a new space and drop in fennel. Leave it to heat up and wilt for 1 minute or more, then stir into the sausage mixture. Sprinkle in 1/2 teaspoon salt.
Clear a little spot in the pan and drop in the chile flakes. Toast the flakes for 30 seconds then stir to combine with the sausage mix. Plop in the tomatoes and stir them into the rest of the ingredients. Leave to simmer for 5 minutes or so while you cook the pasta.
Drop the penne into the boiling water, then bring back to the boil and cook until the penne are al dente. Drain, reserving about 1 cup of the pasta water.
Pour the reserved pasta water into the frying pan and stir well, then bring back to the boil. Reduce to a simmer and cook for about 6 minutes until the flavors have developed, the sauce is thickened but not too thick, and the fennel is soft but not mushy. (Add more water if the sauce reduces too rapidly). Season to taste.