Melt butter over medium heat in a large soup pot. Add onion, salt and thyme and sauté until translucent. Cut cauliflower florets to desired size, and chop stem, removing any tough skin. Add cauliflower to pot and top with enough water to cover completely. Bring to a boil and cook until cauliflower is tender (around 8 minutes). Meanwhile, stir together milk and flour to dissolve all lumps. Reduce heat and slowly add milk and flour mixture. Stir well and simmer until slightly thickened. Turn off heat and stir in cheese. Adjust seasonings and serve.