As someone who only orders cheese on burgers (although with the buns), it means they only want the sandwich to consist of the meat and cheese (hold all other toppings; so if it would normally come with pickles, hold those).

If I go through a typical drive-thru, I order it like this: "cheeseburger plain, with just the cheese" (varied slightly based on the fastfood chain in question). The first plain part removes all the other toppings (or plausibly all the toppings), the with cheese part confirms that you actually do want a cheeseburger and that you only want the cheese. I've found that specific order instruction to be the closest to universally working across all chains, while generating the fewest errors, after ~25 years of testing combinations.