Fluid flow advecting one substance while others are immobilized can generate an instability in a homogeneous steady state of a reaction-diffusion-advection system. This differential-flow instability leads to the formation of steady spatial patterns in a moving reference frame. We study the effects of shear flow on this instability by considering two layers of fluid moving independently from each other, but allowing the substances to diffuse along and across the layers. We find that shear flow can generate instabilities even if the average flow velocity is zero for both substances. These instabilities are strongly dependent on which substance is advected by the shear flow. We explain these effects using the results of Taylor dispersion, where an effective diffusivity is enhanced by shear flow.