Preheat oven to 375 degrees, and line a large baking sheet with aluminum foil or parchment paper.
Make sure and chop the rutabaga and parnips into small pieces, the peppers and onions into larger pieces. (If larger pieces, roast them longer before adding the beef.)
In a large bowl, add all the ingredients together (except fresh thyme and red pepper flakes). Drizzle the mixture with oil. Mix together with your hands or a large spoon. Season with salt, pepper, and dried thyme.
Pour onto the large baking sheet. Cover with foil and bake for 40 minutes. Remove foil and cook an additional 10-15 minutes, until the parsnips and rutabaga are soft. Sprinkle with fresh thyme and red pepper flakes (optional).
Serve right in the pan, with a side of rice!