This is such a great article -- the kind of reading that every legislator and pundit needs to read.
Sure, some games are just toys to play with, but consciously or not, the stereotypes present in all types of media (video games included) shape our view of the world.
Video games often revolve around combat because it's simple, competitive, and adrenaline-inducing. It also helps that every boy plays with pretend guns at some time in their childhood, so it's no surprise that they would continue to play gun-games as they mature. It's not that video games are inherently violent, just that we happen to like violent games.
When it comes to making a violent shoot 'em up, you need something to kill. As a society, we normally don't condone killing people, except as needed to protect ourselves, hence most shooters involve protecting the world from invading enemies. An example that everyone around the world can appreciate is the idea of fighting the Nazis in WW2. This scenario has been played out again and again in books, movies, and of course, video games. Nowadays, the US is less concerned with Nazis and more concerned with assorted terrorists, so it's no surprise that many games now focus on this generic enemy.
The problem is, this simplification leaves many things unsaid. Just as killing Germans in Wolfenstein 3D was left unqualified, so is killing "towel heads" in modern-day Iraqistan. There's no distinction made between civilians and guerillas, there's no concept behind the opposition's motives, there's just "us" and "them".
This is where the problem lies. By generalizing the concept down to "us" and "them", games encourage this type of thinking about foreign entities. Without developing the nuances of the other side, we're unable to distinguish the difference between "foreign" and "bad guy" -- under this generalization, they are one and the same.
We can easily say, "But it's just a game," and yet, it's not just a game -- this, combined with our similarly-biased mass-media, makes up the only window into this foreign entity that many of us ever see. If all we ever know of them is that they (some of them) kill Americans and blow stuff up, then it's only natural to extend that generalization to their entire nation. Of course, this stereotype isn't accurate of the entire country, only of a fringe group, and it's never for the simplistic reasons that we are told, but the fact is that we develop this view anyway.
By not showing both sides of the story, games like Call of Duty and America's Army encourage blind slaughter of entire nationalities by stereotyping them as "the enemy". Even if this simplification is merely part of making the game, the player takes in this mindset while playing it, and without some external rationalization that distinguishes between the game-specific stereotype and the real world, this mindset is what the player adopts in general.