Bring a large pot filled with salted water to a boil. Add penne and cook until tender but still firm, about 12 minutes.
Meanwhile, in a medium sized non-reactive pan, combine tomatoes and chilli flakes. Warm over medium-low heat, breaking up tomatoes if necessary.
Drain pasta and return to hot pan. Add spinach, cream cheese and nutmeg. Cook, stirring, over low heat until spinach wilts, 1-2 minutes. Pour tomato sauce over spinach ziti. Stir and toss gently to mix.