In the military, questioning authority can be a risky proposition. It is a crime under the Uniform Code of Military Justice, or UCMJ, to disobey a lawful order given from any superior commissioned officer or superior noncommissioned or warrant officer. In fact, during time of war, a military member who willfully disobeys a lawful order from a superior commissioned officer can be sentenced to death. The key word here is lawful, because obeying an order which is unlawful can result in criminal prosecution of the one who obeys it.
In the civilian world, the consequences of questioning authority are far less severe. But insubordinate employees who do not follow instructions given by superiors can have their employment terminated. Just as in the military, following instructions that violate civil law can be grounds for criminal prosecution for the employee who follows those instructions.
As an assistant manager working for a prominent national restaurant chain, I faced the dilemma of having to question instructions given by my direct supervisor after he had been accused of sexual harassment by a female employee. The employee in question came to me with a complaint that the general manager, my boss, had touched her inappropriately. I took the complaint very seriously and reported the incident to our human resources department. When an investigation was launched, he told me to back him up as if to indicate that I should take his side on the matter regardless of what I knew to be true. It was clear to me what I had to do: report the facts of the situation as accurately as possible regardless of what my supervisor told me. On the other hand, this was not a job I could afford to lose and had to work day in and day out with someone who could potentially fire me or at the very least make my life miserable. I did report what I knew to be true and, ultimately, he quit his job several weeks later. Although this meant a huge amount of extra work for me having to cover his shifts along with my own, I was greatly relieved that I did not have to face this situation any longer.
Questioning authority ultimately boils down to the moral and ethical beliefs of the individual and whether or not such authority violates those beliefs. Willfully disobeying authority can have disastrous consequences, but when told to do something you know will be destructive or immoral or inflict pain on someone, making the wrong decision can be equally disastrous for someone else.