Prepare flatbread dough. Preheat oven to 475 degrees.
Place a large nonstick skillet coated with cooking spray over medium-high heat until hot. Add onion; saute 4 minutes or until lightly browned. Add mushrooms; sprinkle with thyme and 1/4 teaspoons salt; saute 6 minutes or until tender. Remove from heat; stir in pepper and garlic.
Divide mushroom mixture evenly among 4 flatbread dough ovals; sprinkle 1/4 teaspoons salt over mushroom mixture. Arrange 1/3 cup tomato over each flatbread, and top each with 2 tablespoons cheese. Bake at 475 degrees for 12 minutes or until cheese is melted.