Generally if your entire character is defined by something that makes them incompatible with their own race's culture, you're probably doing something wrong, extenuating circumstances besides; but not everything is that binary. It's okay to question authority in character if you accept the double-edged nature of such behaviour. Anyways, what I believe leowarrior is stating is "don't be a contrarian for the sake of it", so it's less a critique of such characters and more so of the intentions behind them.
Also, unique individualism can occur at any level, not only the highest, and personally if you can implement it at a micro (say, a character's hobbies, mannerism) rather than macro level (political ideologies, allegiances in the global scheme of things), I believe you'll likely find much more success with your characters.