Preheat oven to 400°F. Line a large baking sheet with parchment. Cut the butternut squash into smaller, even pieces. Add to baking sheet with the broccoli and red onion. Drizzle 2 tbsp oil over vegetables. Season with salt and pepper. Bake 20–25 min., until vegetables are tender.
Meanwhile, cook the quinoa according to package directions. Drain, if needed.
In a medium bowl, whisk together the lemon juice, honey, thyme, and remaining 3 tbsp oil. Season with salt and pepper to taste. When roasted vegetables are done, add to bowl, tossing to combine.
Divide quinoa among 4 bowls. Spoon roasted vegetable mixture over quinoa. Top with the dried cranberries and feta cheese.