Heat 2 tablespoons oil in a 12-inch heavy skillet over moderately high heat until hot but not smoking, then saute onions, stirring occasionally, until golden, about 10 minutes. Add garlic and saute, stirring, 1 minute, then transfer onions to a bowl.
Add remaining tablespoon oil to skillet and saute bell peppers, chile, salt, and pepper, stirring occasionally, until bell peppers are tender, about 8 minutes. Add onions and water and bring to a boil, scraping up brown bits from bottom of skillet, then remove from heat.
While peppers are sauteing, cook pasta in a 6- to 8-quart pot of boiling, salted water, stirring occasionally, until al dente. Reserve 3/4 cup cooking water, then drain pasta well in a colander and return to pot. Add onion mixture, reserved cooking water, beans, half of cheese, and half of parsley and toss well.
Serve sprinkled with remaining cheese and parsley.