It was over the TOS but that doesn't mean that they left because they didn't want to be monetized. They were unhappy with the way that Instagram went about it.

If Instagram notified users of a change of TOS and clearly stated that the scheme would be opt-in and perhaps offer a mechanism where users could get a cut of the revenue obtained through the use of photos that they specifically flagged for commercial use, media coverage would have been completely different and I doubt that many users would leave in this scenario (or other more user friendly scenarios).