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People comment anonymously for the same reason we have private ballot boxes. If there is no fear of being penalised professionally for expressing one's true opinions, people are more willing to say what they really think.
Very few people would say something controversial just for the sake of stirring things up- life is too short.
However, many people are aware that they could damage their careers if they expressed an opinion which is at odds with their employers', or referers' interests.