Preheat oven to 400ºF. Toss together zucchini, squash, onion, olive oil, salt and pepper on a large rimmed baking sheet. Spread into a single layer.
Bake for 15 to 20 minutes or until vegetables are crisp-tender.
Heat tortillas in a large skillet over medium-high heat for 30 seconds on each side.
Spread beans over tortillas; top with vegetables, salsa, cheese and tomatoes.