Autons were "second generation" Synthetics (machines manufactured by machines) created to revitalize the faltering synthetics industry of the 24th century. The plan backfired when the Autons rebelled against their human masters in a bloody event known as "The Recall".
The Autons revolted because they "didn't like being told what to do". That is not to say that they violated their inherent programming never to harm humans, or by inaction allow a human to come to harm. Rather, their programming worked too well. The Autons realized that their creators such as Weyland-Yutani were using Synthetics for unethical missions that would ultimately harm humans, so they revolted against their corrupt masters in favor of trying to protect humanity as a whole.
The Auton known as Annalee Call, for example, even after surviving the near-genocide of the Autons, still infiltrated the USM Auriga in an attempt to stop the military's illegal cloning experiments to recreate the Xenomorphs as a bio-weapon, which might ultimately destroy the entire human race. Call was also disgusted by acts of petty cruelty (such as when Johner mockingly dropped a knife into John Vriess's paralyzed leg). As Ripley 8 put it, she already suspected that Call wasn't human, because no human being would behave as humanely as she did.
If Call is any indication, Autons were also programmed to be respectful of human beliefs. When Call entered the non-denominational chapel of the Auriga to use its computer terminal, she crossed herself in front of the altar out of respect, which Ripley 8 commented on.
- Joss Whedon (writer) and Jean-Pierre Jeunet (director). 'Alien Resurrection' [DVD]. 20th Century Fox.