I think perhaps Olympic TKd does have a problem, the general public is far more aware of martial arts these days due to the popularity of martial arts films and their stars, there's few who haven't watched Jackie Chan for instance however they are generally ignorant of the differences between martial arts. For example people who know me obviously know I do martial arts but it gets called various things, Judo, karate, Kung Fu and even jap slapping, I've been asked several times now about the TKD that is being shown from the Olympics. The first thing is always why is it just kicking, that's not the martial arts they see normally in films etc. It's not what they see whenever a martial arts demo is on. That's TKD first image problem. If people are switching on to watch a martial art they want it to be what they consider a martial art which to many now is probably a Chinese one, punches, strikes and fancy kicking.
Will the Cuban incident harm TKD, yes but maybe not in the way you imagine. I've been on another site where everyone was saying well why couldn't the ref defend himself, ok the kick would have taken him by surprise but even so instinctively you tend to block or move. Martial artists in the general public's eyes ought to be able to defend themselves! That's the perception and what is being voiced by non martial arts people. Rightly or wrongly that's what's out there.
The petulance and bad sportsmanship is being taken as just that, one bad apple only.