To illustrate the physics behind the relation, let's take a physical example of a charged particle moving in the $x$-$y$ plane, in the presence of a magnetic field $B$ pointing in the $z$ direction. We want to interpret the relation
$$
[D_x,D_y] = i q F_{xy} = i q B \,,
$$
as an operator acting on the wavefunction $\psi$ of a particle of charge $q$.
Now, $\psi$ has an unphysical phase, because it changes under gauge transformations:
$$
A_\mu \longrightarrow A_\mu +\partial_\mu\lambda,\qquad \psi \longrightarrow e^{-iq\lambda}\psi
$$
However, relative phases are important for interference effects. The covariant derivative gives a gauge invariant way to say that the phase of the wavefunction is "constant", $D_\mu \psi=0$.
Now, let's say the particle has two possible paths to get from the origin $x=y=0$ to a point $x=y=\epsilon$: either it moves first in the $x$ direction to $x=\epsilon$, $y=0$ and then in the $y$ direction, or the other way round. The commutator $\epsilon^2[D_x,D_y]\psi$ compares how the magnetic field affects the wavefunction differently for the two paths: we get $i q B \epsilon^2 \psi$, which tells us that there's a small relative phase $e^{i q B \epsilon^2}$.
The relative phase can lead to interference effects from a superposition of the two paths, which is the Aharonov-Bohm effect. For a finite path, the relative phase will be $q$ times the total magnetic flux $\int\! B$ between the paths. More covariantly, this can also be expressed as a surface integral of $F_{\mu\nu}$, or using Stokes' theorem, a line integral $\oint A_\mu dx^\mu$ following the two paths in opposite directions. While $A_\mu$ is not gauge invariant, this integral along a closed path (a `Wilson loop') is. The commutator relation is therefore a version of Stokes' theorem, relating an integral round a loop to a flux through it, for infinitesimal loops.