I use clip-ons because I don't have a pedalboard. Now, I often set up pedals (on the floor, obviously) but only one to three, and I don't want to add yet another -- especially a "no fun" pedal, as JimmyM called it.
More importantly: I sometimes play gigs in cramped conditions where it would be awkward at best to set up pedal(s). Then there are gigs where I don't have time for whatever reason(s). And I sometimes play multi-band festival gigs where backline is provided: for those I just go K.I.S.S. and use my bass into backline, nothing else.
Bottom line:
for me, it's a no-brainer to use a clip-on and not pedal.