Preheat oven to 375 degrees. Coat 12 standard-size muffin cups with cooking spray. Evenly distribute broccoli and roasted red pepper among the muffin cups. Top with shredded cheddar cheese.
In a large liquid measuring cup, whisk together eggs, milk, salt, and pepper. Carefully pour the mixture into each cup. Bake the eggs until puffed and set in the center, about 15 minutes. Let frittatas cool in pan about 5 minutes. Use a rubber spatula to remove the eggs from the cups. (Frittatas can be stored in the fridge for 3 days or frozen in a zip-top bag. Reheat in the microwave on high power for 1 minute per frittata before serving.)
To serve, place a frittata on a toasted whole-wheat English muffin with a dollop of storebought pesto, if desired