Preheat the oven to 350F. Lightly salt eggplant slices and place in a colander for 10 minutes. Rinse and dab dry with a towel.
Put onion, peppers, garlic, salt, and pepper in a large bowl. Dress with olive oil and toss well. Place them on a baking sheet and roast for 35 minutes, turning occasionally. Add eggplant during the last 15 minutes and turn once.
Meanwhile, bring a pot of water to a boil. Cook penne for 10 minutes and drain.
Serve veggies over the pasta and garnish with cheese.