Gently fry onions, garlic, and chili flakes in olive oil in a large saucepan for about 10 minutes, or until soft and golden.
Meanwhile cut off the tough skin of the butternut squash. Scrape out and discard the seeds, then roughly chop the flesh and stir it into the sauteed onions. Cover and continue to cook, stirring occasionally, until the squash begins to soften.
Add the stock, herbs, and parmesan rind and simmer gently for 45 minutes, or until the squash is meltingly soft.
Discard the herbs and Parmesan rind, scraping any gooey cheese into the soup.
In a blender, (careful with the hot liquids) process the soup, add the creme fraiche, and season to taste.