I admit I'm using "subset" in the colloquial sense, meaning "a set that's missing some of the elements in its superset", which is not technically the correct definition (every set is a subset of itself, i.e. a subset doesn't have to be missing anything). So technically a subset does not imply fewer elements. Is that what you're getting at?
I'm not particularly well versed in set theory, so maybe I'm just misunderstanding your point about countability.
This is the important point where you are wrong. For a simpler to explain example : the naturals are a subset of the integers, and yet the set of all integers is exactly as big as the set of all naturals. We say this because we can actually find a natural number that corresponds to every integer number: 0:0, 1:+1, 2:-1, 3:+2, 4:-2,... A slightly more complicated construction exists for the naturals compared to the rationals: they are also the same size.
However, it can be shown that the same can't be done between the naturals and the reals, or even any real interval. So, by this definition, there are more real numbers between 0 and 1 than there are in the entire set of natural numbers.
Lots of subsets of the reals are uncountable, most notably if the rationals are countable and you split the reals into rationals and irrationals, the irrationals have to be uncountable. Otherwise you'd be forced to say that the union of two countable sets could be uncountable, which isn't true (if you have two countable sets you can automatically produce an enumeration of the union).