In a medium bowl combine the balsamic vinegar, olive oil, rosemary, garlic, lemon zest and red pepper flakes. Whisk to combine and pour into a 1-gallon resealable food storage plastic bag. Put the chicken thighs in the bag and seal it. Turn to ensure that the chicken is evenly coated, then refrigerate, turning occasionally, for 2 to 4 hours.
Preheat a grill to medium-low and brush the grates lightly with an oil soaked cloth. Remove the chicken from the marinade and pat dry. Season the chicken well on all sides with salt and pepper, then place on the grill, skin side down. Cook the chicken about 8 to 10 minutes, turn and continue to cook an additional 8 to 10 minutes, or until the chicken is cooked through. Remove from the heat and serve while hot.