The set of rational numbers in $[0,1]$ is used as the counterexample that shows not every midpoint convex set is convex. To see the fact notice that the set of rational numbers in $[0,1]$ is midpoint convex since for any pair of rational numbers $x,y$ in $[0,1]$ $\frac{x+y}{2}$ is a rational number in $[0,1]$.
Now the question is how to show the set of rational numbers in $[0,1]$ is not convex.