Cylinder stubs of finite length, mounted in a wall-normal manner on a flat plate, exert considerable control on their wake when rotating around their central axis. The present paper investigates these effects with linear stability theory and a direct numerical simulation. Three configurations are considered: evenly spaced corotating roughness elements, as well as positive and negative counter-rotating roughness pairs. Here, ‘positive’ and ‘negative’ are defined in accordance with the induced high- and low-speed streaks, respectively. A primary feature of the rotating-cylinder-induced wake is a ‘dominating inner vortex’ (DIV), which intensifies the lift-up effect and creates high-amplitude streaks. Linear stability analysis shows that the modified streaky flow is capable of effectively stabilizing Tollmien–Schlichting (TS) modes. The mechanism of TS mode stabilization, as found by a perturbation kinetic energy analysis, is attributed to the reduction of the wall-normal perturbation production. On the other hand, an inviscid inflectional instability mode related to the presence of the roughness appears which destabilizes the boundary-layer flow, primarily due to an increase in wall-normal perturbation energy production, but also due to increasing spanwise energy production, depending on the case. The inflectional instability roughness mode is more amplified with thicker cylinders since the induced DIV tends to support longer-living inflection points. Regarding an imaginable laminar–turbulent transition delay, positive rotating thinner roughness pairs would be preferable.