Experimentally produced graphene sheets exhibit a wide range of mobility values. Both extrinsic charged impurities and intrinsic ripples (corrugations) have been suggested to induce long-range disorder in graphene and could be a candidate for the dominant source of disorder. Here, using large-scale molecular dynamics and quantum transport simulations, we find that the hopping disorder and the gauge and scalar potentials induced by the ripples are short-ranged, in strong contrast with predictions by continuous models, and the transport fingerprints of the ripple disorder are very different from those of charged impurities. We conclude that charged impurities are the dominant source of disorder in most graphene samples, whereas scattering by ripples is mainly relevant in the high carrier density limit of ultraclean graphene samples (with a charged impurity concentration < 10 ppm) at room and higher temperatures.