We perform direct numerical simulations of the flow through a model of deformable porous medium. Our model is a two-dimensional hexagonal lattice, with defects, of soft elastic cylindrical pillars, with elastic shear modulus G, immersed in a liquid. We use a two-phase approach: the liquid phase is a viscous fluid and the solid phase is modeled as an incompressible viscoelastic material, whose complete nonlinear structural response is considered. We observe that the Darcy flux (q) is a nonlinear function - steeper than linear - of the pressure-difference (Delta P) across the medium. Furthermore, the flux is larger for a softer medium (smaller G). We construct a theory of this super-linear behavior by modelling the channels between the solid cylinders as elastic channels whose walls are made of material with a linear constitutive relation but can undergo large deformation. Our theory further predicts that the flow permeability is an universal function of Delta P/G, which is confirmed by the present simulations.