Passengers, quite simply, shows us the difference between humans and robots. While the latter may lay claim to cognitive intelligence, they fall short and come nowhere close to our capacity for morality, empathy, love and the entire gamut of human emotions - some of our finest and worst qualities as humans; especially as regards decision making, which often have several different complicated layers other than the logical.
When Jim contemplates waking Aurora prematurely, it was borne of a selfish need for companionship, but which to Arthur, the android bartender, seemed only logical - a fitting solution to a pressing problem without the unnecessary handicap called morality.
Again, when Aurora falsely declares that there aren't any secrets between Jim and her, Arthur sees fit to correct that impression, not for the sake of right or wrong, but because of how illogical the claim was.
He's indifferent to how either feels. He is incapable of comprehending them, seeing events only through the narrow lens of logic. Whereas Gus, a human, could empathise with both of them - Jim, for the years of isolation he would have had to endure due to no fault of his, and Aurora, for her righteous anger at the one who decided her future without her consent.
The movie portrays in stark tones this messy business called humanity, all its strong points and imperfections. It doesnโt always make sense nor is it perfect despite the best intentions (Avalon's malfunction paints a ready picture). And perhaps, therein lies the answer - it's not meant to make sense nor be perfect, we are just to do our part, our share of good (hopefully not bad!) and move on.