Place rutabaga in a large saucepan, and cover with water; bring to a boil. Reduce heat, and simmer 25 minutes or until tender. Drain.
While rutabaga cooks, melt butter in a large nonstick skillet over medium-high heat. Add shallots; sauté 2 minutes. Add 1 cup chicken broth, Madeira wine, honey, and salt; bring to a boil. Reduce heat, and simmer until reduced to 1/2 cup (about 20 minutes). Add rutabaga, fresh thyme, and black pepper to pan; toss gently to coat.