It has more to do with that stories in most popular media (and particularly games) rarely deal with the other side. The dark side.
That's why you haven't played a World War 2 game from the perspective of a german soldier who is forced to fight for his country, regardless if he believes in the cause or not. Nobody would dare make a game were you play a guard in a concentration camp, or play a Panzer tank operator stranded in the russian winter waste as you slowly decay to frost and hunger.
Playing as the good guys, the heroes is always the easy sell, and so that is the fiction that is mostly made. When your dealing with sci-fi, fantasy or the supernatural and you have foreign races and/or species, its easiest to bank on humans for their relateability, or something close to it (humans with improvements, or minor alterations).
It's like pop music. Nothing wrong with it, easily absorbed by the masses, with not a big calling from the mainstream to experiences stories that are difficult and uncomfortable or hard to stomach. It's easier to go for a easily digestible experience than something which might be profound but will leave you feeling like shit.
We all know this feeling from movies were we are suggested to watch something really depressing or fucked up, but we end up going for Mission impossible ghost protocol or the avengers instead. Nothing wrong with that. It's just about knowing what you want, and not hating something for being something else.