I find that it helps to recast Cantor's argument as constructing something.
Specifically, we define a function $F$ from $\{$maps from $\mathbb{N}$ to $\mathbb{R}\}$ to $\mathbb{R}$, that is, from lists of reals to reals. This $F$, in particular, "does something" to every list.
We now prove a fact about the $F$ we've just constructed: namely, that - regardless of what list $f$ we start with - $F(f)$ is not in $ran(f)$.
We have now used the object $F$ we've constructed to show that no counting of $\mathbb{R}$ exists. But this depends crucially on the part of the previous paragraph that says
regardless of what list $f$ we start with
and it's here that your idea breaks down. What you've shown is that there is some list of naturals which is not surjective; what you would need to do is show that every list of naturals fails to be surjective.
EDIT: Let me add the following, which I hope will help.
You are quite right that "is a proper subset of" does not imply "is smaller than". So just knowing that $ran(f)\not=\mathbb{R}$ for some listing $f$ of reals does not mean that $ran(f)$ is smaller than $\mathbb{R}$!
However, again, note that Cantor has shown that every $f:\mathbb{N}\rightarrow\mathbb{R}$ has the property that $ran(f)\not=\mathbb{R}$. It is the fact that every $f$ has "small range," not the fact that some $f$ has "small range," which proves that $\mathbb{R}$ is uncountable.
One way to think about this that might help is the following. Suppose $f:\mathbb{N}\rightarrow\mathbb{R}$. By Cantor's argument, we know $ran(f)\not=\mathbb{R}$. But couldn't $ran(f)$ have the same size as $\mathbb{R}$, nonetheless?
Well, suppose it did - that is, suppose there were a surjection $g$ from $ran(f)$ to $\mathbb{R}$. Then think about $g\circ f$. This is a function from $\mathbb{N}$ to $\mathbb{R}$, and - by assumption on $g$ - it is surjective.
But that's a problem! Cantor's argument shows that no map from $\mathbb{N}$ to $\mathbb{R}$ can be surjective. So we have a contradiction.
So not only is $ran(f)$ a proper subset of $\mathbb{R}$, for every $f:\mathbb{N}\rightarrow\mathbb{R}$, but $ran(f)$ is always strictly smaller than $\mathbb{R}$!
This is an interesting phenomenon, that happens a lot in mathematics: a weak universal statement can sometimes "strengthen itself." Basically, what this looks like is the following:
We prove "Every Foo has the weak Bar property."
Now, in general, the weak Bar property does not imply the strong Bar property.
However, from a Foo without the weak Bar property, we can build a Foo without the strong Bar property.
So by the first bullet point, we've in fact shown: Every Foo has the strong Bar property.
(The following paragraph is subjective, and you may not find it helpful - feel free to ignore it if so. For contrast, consider the phenomenon of strengthening the induction hypothesis in proofs by induction: you want to prove "All $n$ have property $\alpha$" by induction, but the obvious attack doesn't work - so instead you prove "All $n$ have property $\beta$" for a stronger property $\beta$! And, even though this should be harder to prove (you're proving a stronger result after all), it winds up being easier. That is, to prove a weak thing, you find yourself having to prove a strong thing. What's going on above is sort of the dual of this: we prove a weak thing, and then that immediately implies the strong thing!)