In a glass baking dish or large resealable plastic bag, combine the soy sauce, honey, garlic, ginger, and pepper flakes (if using). Add the salmon, skin-side up. Cover and refrigerate for 30 minutes.
Heat broiler on high. Transfer the salmon to a foil-lined broiler pan, skin-side down. Broil until the salmon is the same color throughout and flakes easily, 7 to 10 minutes. If desired, pour the marinade into a small saucepan and boil for 1 minute. Spoon the sauce over the salmon.