Combine all of the ingredients, except the red pepper flakes) in a small saucepan over medium-high heat. Bring the mixture to a boil and then reduce to a simmer. Allow the sauce to simmer until reduced by half, 20 minutes. Pour the sauce into a bowl through a small sieve to remove the onion and pepper. If you want the sauce to have some spice, return the strained sauce to the pan over medium heat. Add red pepper flakes to taste and heat for 1 minute more.) Chill the sauce in the refrigerator until ready to use.