You do your best within the constraints you're given, which is what is being said in your example. You are welcome to make your arguments for or against a decision (as far as office politics allow), but just as there is a breaking point for you being told to do something you feel is "incorrect," there is a breaking point where you become "the guy who always gives them a hard time."

Soft skills are important as technical when you're working with others. You have to pick and choose your battles. Don't confuse a platitude with a literal decree. Does that make more sense?