The advantage I see with Toslink (S/PDIF optical) is the galvanic isolation. If you are receiving RF interference through single ended cables, or have an otherwise noisy source, Toslink is an easy way to eliminate that.
A disadvantage of Toslink is that it is limited by Specification to 96 kHz. If you desire files with higher sampling rates, S/PDIF coaxial can go to 192 kHz, and USB can go to higher sampling rates.