My problem doesn't arise only when comparing sets such that one strictly contains another. I can "prove" to myself that there are more rational numbers between any two integers than there are natural numbers, because I can account for every last natural number with a rational between the two integers and have some rationals left over. I can also read other people "proving" that the rationals (between two integers or altogether, it hardly matters) are "countably infinite" and therefore not more numerous than the integers, because they can be lined up. I get that the second way of arranging them exists. It's just not at all clear why it's a better way of arranging things, or why the answer it generates about the relative sizes of the sets in question is a better answer.