I think GP's point wasn't that their secrecy makes them deserve negative public opinion, rather that a policy of secrecy in general makes it rather difficult to believably deny allegations of questionable behavior -- that secrecy is a double-edged sword.

Also, I don't think it's entirely fair to construct a black-and-white dichotomy between government and private company. Companies working on government contracts are by definition somewhere between the two, so perhaps it's fair to demand transparency somewhere in between? I don't know where to draw those lines, I'm just trying to point out that there isn't, logically, much room for absolute arguments about private vs public on this particular topic.