I see the ATC/Pilot relationship as a team. There is a job to be done and each has their role. As a pilot I have never considered ATC as the authority of what I must do, that is my call as PIC, but if I can safely execute their instructions then I know that the job will get done. The key word here is "safely" and so I always have that in mind.
I also know that if ATC requests me to do something then they expect it to happen, promptly and accurately and not to do so at best makes the job of the controller more difficult and at worst put safety at risk.
I don''t think this article tries to create a hostile relationship at all. Instead I think it highlights the fact that ATC is not the boss. As PIC you are the boss but not to do as ATC requests requires a very sound reason and we must communicate our intentions clearly if we cannot comply. I think this article makes those points and was well put.
