In response to Joel's comment, here is an argument showing that it is consistent that every ccc poset of size $\omega_1$ is the union of its nonatomic countable complete subposets.
Suppose $\text{MA}_{\omega_1}$ holds. It follows that there are no Suslin algebras, so any ccc poset must add a real. Furthermore, by a theorem of Pawlikowski, any poset of size $<\mathbf{add}(\mathcal{M})$ that adds a real must add a Cohen real. Therefore any ccc poset of size $\omega_1$ adds a Cohen real.
Now let $\mathbb{P}$ be such a poset and take $p\in\mathbb{P}$. Let $p\in A\subseteq\mathbb{P}$ be a (countable) maximal antichain. By the fact above, the cone $\mathbb{P}\upharpoonright p$ adds a Cohen real, so the usual forcing theory gives us a complete subposet $\mathbb{Q}\subseteq\mathbb{P}\upharpoonright p$ which is forcing equivalent to $\mathrm{Add}(\omega,1)$. Now, this equivalence and the fact that $\mathbb{Q}$ is ccc yield that there is a countable dense $\mathbb{Q}'\subseteq\mathbb{Q}$. Taking all of this together, $\mathbb{Q}'\cup\{p\}\cup A$ is a countable complete subposet of $\mathbb{P}$ containing $p$.
Janusz Pawlikowski,
MR 1825187 Cohen reals from small
forcings, J. Symbolic Logic
66 (2001), no. 1, 318--324.