Think of it like this:
Isaac Asimov's "Three Laws of Robotics"
- A robot may not injure a human being or, through inaction, allow a human being to come to harm.
- A robot must obey orders given it by human beings except where such orders would conflict with the First Law.
- A robot must protect its own existence as long as such protection does not conflict with the First or Second Law.
http://www.auburn.edu/~vestmon/robotics.html
The androids are roughing up Rodrigo Santoro when William escapes but he's smiling at the end of the scene because he knows he's not really in any danger. Now remember that every potentially dangerous item is controlled by the company. In one scene a fire wasn't started because the only host with the correct psychological blocks necessary to be allowed to handle an axe wasn't present. The guns don't function correctly when used against a human. The explosives Ed Harris used had to be authorized before they were allowed to work (also meaning that the nitro wasn't going to blow up on that train regardless of whether Dolores shot at it).