Peel the butternut squash and halve it lengthwise. Remove and discard the seeds and slice the squash crosswise 1/2 inch thick. Place the squash in a sheet pan, drizzle with olive oil, and sprinkle with 1 teaspoon salt and 1/2 inch black pepper. Toss together and spread out the slices in one layer. Roast for 25 to 30 minutes, tossing occasionally until browned and tender.
Meanwhile, melt the butter in a small (8-inch) sauté pan over medium heat. Add the sage, red pepper flakes, 1/4 teaspoon salt, and 1/4 teaspoon black pepper and cook for 2 to 3 minutes, swirling often until the butter begins to brown and has a nutty aroma. Remove from the heat.
Place the squash on a serving plate. Gently reheat the brown butter and spoon it over the squash. Lightly sprinkle some lemon zest on top, sprinkle with salt, and serve hot.