Different transports will output digital signals of varying quality. The theory is certainly just 1's and 0's, but timing (e.g. jitter), signal fidelity, signal noise, shield noise, picked up interference, physics (a digital signal is still an analog thing), and circuit or algorithm implementation nuances can all affect the signal.
So, all parts of the equation can matter: the transport, the cable, the DAC. Obviously, some equipment (and their implementations) can better handle a wider range of situations, or worse situations. For example, hard disks have better error detection and correction than CD-ROM drives. Cables with better shielding, or a balanced configuration, will do better at rejecting noise. And DACs that use their own internal clock will be less susceptible to high jitter S/PDIF signals.