Bring quinoa and water to a boil in a saucepan. Reduce heat to medium-low, cover, and simmer until quinoa is tender and water has been absorbed, 10 to 15 minutes. Set aside to cool.
Whisk olive oil, lime juice, cumin, 1 teaspoon salt, and red pepper flakes together in a bowl.
Combine quinoa, tomatoes, black beans, and green onions together in a bowl. Pour dressing over quinoa mixture; toss to coat. Stir in cilantro; season with salt and black pepper. Serve immediately or chill in refrigerator.