Preheat the oven to 425 degrees. Cut peppers in half, removing stems and seeds, and place face down on baking sheet. Once skins start to pull away, change oven to broil for a few minutes, then remove from oven and let cool. When peppers are cool, remove skins.
Combine onions, shallot, olive oil, red pepper flakes and roasted cumin in a non-stick pan. Cook over medium high heat until onions translucent, about 5 minutes.