The present work proposes a Chebyshev-collocation Fourier-Galerkin pseudospectral method for simulating unsteady, three-dimensional, fluid flows in cylindrical geometries with pressure-driven flow through permeable boundaries. Such systems occur in diverse applications and are challenging to simulate due to an additional velocity-pressure coupling on the permeable walls through Darcy's law. The present work extends the projection method of Raspo et al. (2002) to assure Darcy's law is satisfied exactly. A multidomain solver allows the efficient treatment of open boundary conditions that necessitate permeability buffers and a sponge layer. The method is spectrally convergent, and we demonstrate that pressure-prediction is necessary to obtain second-order temporal accuracy. The ability of the method to simulate complicated physical systems is demonstrated by simulating subcritical and supercritical flows in rotating filtration in Taylor-Couette cells. For subcritical cases, numerical results show excellent agreement with analytical solutions. For supercritical cases, the numerical method accurately resolves convectively and absolutely unstable flows with traveling toroidal and helical vortical structures that are in good agreement with a local linear stability analysis and experimental observations.