Lemma: Let $(X,d)$ be a metric space. For each $n \in \{1,2,3,\ldots\}$ there is (by Zorn's lemma) a maximal (by inclusion) set $D_n$ such that for all $x,y \in D_n$ with $x \neq y$, we have $d(x,y) \ge \frac{1}{n}$. If all $D_n$ are at most countable, then $X$ is separable.
Proof: We'll show that $D = \cup_n D_n$ is dense (and is countable when all $D_n$ are), and so pick any $x \in X$ and any $r>0$ and we'll show that $B(x,r) \cap D \neq \emptyset$. Suppose not, then find $m$ with $\frac{1}{m} < r$. Then from $B(x,r) \cap D = \emptyset$ we know that
$d(x, y) \ge \frac{1}{m}$ for all $y \in D_m$ (or else $y \in D \cap B(x,r)$), and then $D_m \cup \{x\}$ would contradict the maximality of $D_m$. So the intersection with $D_m$ and hence $D$ is non-empty, and so $D$ is dense.
(The above is the heart of the proof that a ccc metric space is separable, as $X$ ccc implies that all $D_m$ are countable, as the $B(x,\frac{1}{m})$, $x \in D_m$ are a pairwise disjoint open family of non-empty sets.)
Now suppose that $(X,d)$ is countably compact. Suppose for a contradiction that $X$ is not separable. Then for some $m \ge 1$ we have that $D_m$ (as in the lemma) is uncountable.
Fix such an $m$.
Now $D_m$ is discrete (clear as $B(x,\frac{1}{m}) \cap D_m = \{x\}$ for each $x \in D_m$) and closed: suppose that $y \in X\setminus D_m$ is in $\overline{D_m}$, then $B(y, \frac{1}{2m})$ contains infinitely many points of $D_m$ and for any $2$ of them, say $x_1, x_2 \in D_m$, we'd have $d(x_1, x_2) \le d(x_1, y) + d(y,x_2) < \frac{1}{m}$ contradiction (as points in $D_m$ are at least $\frac{1}{m}$ apart). So $D_m$ is closed and discrete (as an aside: being uncountable this would already contradict Lindelöfness of $X$; this shows that a Lindelöf metric space is separable, e.g.), but we want to contradict countable compactness, which is easy too:
Choose $A \subseteq D_m$ countably infinite (so that $A$ is closed in $X$, as all subsets of $D_m$ are), and define a countable open cover $\mathcal{U} = \{B(p, \frac{1}{m}): p \in A\} \cup \{X\setminus A\}$ of $X$ that has no finite subcover: we need every $B(p,\frac{1}{m})$ to cover $p$ for all $p \in A$.
This contradiction then shows $X$ is separable (and thus has a countable base ,is Lindelöf etc. finishing the compactness).
The crucial fact is that all of the following are equivalent for a metric space:
- $X$ has a countable base.
- $X$ is separable.
- All discrete subspaces of $X$ are at most countable.
- All closed and discrete subspaces of $X$ are at most countable.
- $X$ is ccc.
- $X$ is Lindelöf.
In the above I essentially did "not (2) implies not (4)" implicitly. The fun is that countable compactness implies (4) easily (such closed discrete subspaces are even finite) and thus we get Lindelöfness "for free". Also implicit in the above proof is that every countably compact space is limit point compact.
In fact, I don't see a reason to worry, as all compact (or Lindelöf) metric (or metrisable) spaces are separable (just take a finite (or countable) subcover of the cover of all $\frac{1}{n}$-balls, for every $n$, and collect the centres used in all these subcovers to get a countable dense subset of the space).
So compact is more than enough to apply your result on separable metric spaces.
Best Answer
A counterexample is the "Baire space" $\mathcal{N} = \mathbb{N}^{\mathbb{N}}$. This is one of the main examples of a Polish space: a separable, completely metrizable space.
One fact about this space is that all compact subsets have empty interior, that is, all compact subsets are nowhere dense. By the Baire Category Theorem, $\mathcal{N}$ is not the countable union of nowhere dense subsets, and so together with the above fact it cannot be $\sigma$-compact.
See also this question and its answer for more details: