The divergence of a vector field $E$ at a point $p$ is determined by the behaviour of $E$ in the neighbourhoods of $p$.
Choose a neighbourhood $U$ of $p$ (it can be as small as you want), and consider the field lines of $E$ in $U$. Since the field is weaker away from the charges, some field lines are going to be "stronger" than others. The divergence of $E$ at $p$ measures the lines that concentrate towards $p$ minus the lines that point outwards $p$.
In this case, the lines that concentrate towards $p$ are coming from the charges, so they are stronger than the lines that point away from $p$. But the lines that point away are more abundant (i. e. they cover a wider volume) than the stronger lines. This is easier to see in the case of a field generated by a point charge $q$:

In this picture, the yellow lines are field lines, and the blue circle is the neighbourhood $U$. The grey line separates the lines closer to the charge (they are stronger, and some of them are pointing towards $p$) and the ones away from $q$ (all of them point outwards from $p$, and they cover a larger part of $U$, but they are weaker).
The general case is pretty much obtained by adding up (integrating) the fields spanned by infinite point charges, but divergence is linear, so the divergence of the sum will be equal to the sum of the divergences (which are zero).