I don’t know what argument you used, but here’s the easiest one that I know.
Let $U$ be a non-empty open subset of $\Bbb R$. Define a relation $\sim$ on $U$ as follows: for $x,y\in U$, $x\sim y$ iff either $x\le y$ and $[x,y]\subseteq U$, or $y\le x$ and $[y,x]\subseteq U$. It’s not hard to check that $\sim$ is an equivalence relation. For $x\in U$ denote by $U(x)$ the $\sim$-equivalence class of $x$. Then $U(x)$ is order-convex and open in $\Bbb R$.
$U(x)$ is order-convex. Suppose that $y,z\in U(x)$ with $y<z$. If $x\le y$, then $[y,z]\subseteq[x,z]\subseteq U(x)$. If $z\le x$, then $[y,z]\subseteq[y,x]\subseteq U(x)$. And if $y<x<z$, then $[y,z]=[y,x]\cup[x,z]\subseteq U(x)$.
$U(x)$ is open. Suppose that $y\in U(x)$. Suppose that $x<y$. $U$ is open, so there are $u,v\in\Bbb R$ such that $y\in(u,v)\subseteq U$. Let $w\in (y,v)$ be arbitrary. Then $[x,w]=[x,y]\cup[y,w]\subseteq U$, so $y\in(x,w)\subseteq U(x)$. The case $y<x$ is entirely similar, and the case $y=x$ is trivial.
Thus, $\{U(x):x\in U\}$ is a partition of $U$ into order-convex open sets. Since each must contain a rational numbers, there are only countably many of these sets.
Note that the result fails if you insist on having bounded open intervals. If $(a,b)$ is one of the intervals in the decomposition of $U$, no other interval can contain either $a$ or $b$. Thus, if $U$ contains an open ray, $U$ cannot be decomposed into pairwise disjoint bounded open intervals.