You're right, but I've always been under the impression that the DAC handles the ground loop (if applicable) during the first stage of input. I suppose that could be totally wrong. I've never had to deal with that sort of problem because my sound equipment is segregated on it's own power source since other things affect it (like CFL bulbs :-\). Either way, I agree if ground looping is an issue, then you should add isolation, but this still doesn't make it a pro or con for the whole fiber vs usb since fiber cost significantly more (not just in the cable, but converting all equipment if you need to). My other comments were based on the assumption that everything is "clean".
it actually really depends on your amp's ground implementation. i had an amp that had a ground loop issue (improperly implemented/isolated ground i believe, confirmed to be ground loop issue by using a 3-prong to 2-prong cheater plug on the amp, noise went away) which i have tried with many dacs (including ones with dedicated power supply and ones with battery power), and the ground loop issue is always there with that amp as long as im not using optical. dacs with dedicated power supply and battery did help, the humming noise is considerably lower than ones without (ie drawing power from usb), but the issue is definitely still there and the only way i've found to completely get rid of the noise is by using optical between the pc and dac (admittedly i did not try cutting/taping over the ground and power pins on the usb cable for self-powered dacs, but im not sure if that'll make a difference)
when it comes to dacs, it is better to assume that not everything is clean. in fact, i would start assuming that the pc power is not clean as that is more often than not the case. ground loop issue may or may not be an issue, depending on your dac and amp (personally i have not encountered that problem with any of the other amps that i got after), so the benefit of galvanic isolation that optical provides completely depends on your setup (some dacs/amps even have a special ground-lift switch to completely get rid of the problem without resorting to optical).
as far as cost is concerned, i think usb and toslink are at pretty much the same level so as to not be a concern for most. a good async usb receiver/controller chip (eg xmos) could cost a lot more than a good toslink DIR. optical cables are also not really more expensive than usb (you can get 3 ft for ~$3-4).
to answer OP's question more directly. for playback of materials up to 24/96 (or 24/196 for certain dacs), usb and optical should be effectively the same in quality, provided both use quality components and implemented properly (ie good usb receiver and good optical DIR). usb has the added advantage of supporting much higher bitrates (eg DSD/DXD, but only if your dac supports it), which optical cannot do. usb also provides more consistent playback quality regardless of source device, as the optical output quality of certain devices (eg airport express?) is not as good as others and can cause problems such as massively increased jitter. on the other hand toslink has the benefit of providing complete galvanic isolation, which eliminates any possibility of ground loop issues (if there are any to begin with)
TL;DR: if you need super high bitrate playback, or if your optical source is lower quality, use USB. if you have a ground loop issue, use optical. otherwise either should be fine (provided your dac implements both well enough)
ps: and if you want DSD but have a ground loop issue? get an usb ground isolator and use usb