Cook penne according to package directions. Meanwhile, in a large nonstick skillet over medium heat, cook onions in butter for 8-10 minutes or until lightly browned. Add the thyme, basil and salt; cook 1 minute longer. Add 1 cup cream, wine or broth, and tomato paste; cook and stir until blended.
Combine flour and remaining cream until smooth; gradually stir into the onion mixture. Bring to a boil; cook and stir for 2 minutes or until thickened. Stir in 1/4 cup cheese. Drain penne; toss with sauce. Sprinkle with remaining cheese.
