Traction is an issue. In creeks where the water is clear and not deep, no shoes might be fine, but in fast running rivers where you might be at least knee deep and can't see anything at all, one mistep and you can easily go over. I have a dislocated shoulder that proves how important traction is and that happened in a parking lot.

If you can't see the bottom, as I wrote, you have no idea what you are stepping on. To be honest, I couldn't care less what other people do as long as they aren't with me. I would never let anyone with me cross water with their shoes off. To me, it isn't worth the risk. I was hiking alone much of the time, so risk management was a high priority for me.

I don't mean to come across as mean spirited either, but for the conditions I was hiking in, I never saw anyone take off their boots and for good reason.