Preheat oven to 400°F. Butter 11x7x2-inch glass baking dish. Melt 3 tablespoons butter in heavy large skillet over medium-high heat. Add shallots; sprinkle with salt and pepper. Cover and cook 5 minutes, stirring often. Reduce heat to medium. Cook, covered, until shallots are deep brown, stirring often, about 6 minutes.
Meanwhile, cook macaroni in large saucepan of boiling salted water until just tender but still firm to bite, stirring occasionally; drain well. Reserve pan. Bring half and half and hot sauce to simmer in same saucepan over medium heat. Toss cheddar cheese and flour in medium bowl to coat; add to half and half mixture. Whisk until sauce is smooth and just returns to simmer, about 2 minutes. Mix in pasta. Season with salt and pepper.
Spread pasta mixture in prepared dish. Top with shallots, then goat cheese. Sprinkle with pepper. Bake until heated through, about 15 minutes.