Actually, only a few missions in MW3 have you fighting the Russian army (who, by the way, are actively invading most of Europe and the US. It isn't like we are blowing up innocent bystanders here). The grand majority of the game is spent fighting Makarov's men, who are most definitely terrorists first, Russians second.
Why do Russians make a good enemy? For the exact reasons you mentioned. Of all the countries America has been at war with, Russia was our enemy the longest, and came the closest to a full scale nuclear war. Despite our friendly relationship with Russia now, it doesn't change the fact that within our parents lifetimes we were in a conflict that could have annihlated all of us. Heck, I'm sure some of the posters on this board can remember a time when Russia was THE bad guy. That sort of thing doesn't just fade out of public conciousness. Nazis are about the only stand in that works as well, being both a classic American enemy AND pretty much unarguably evil. But its been a long time since WWII, they just don't have the same resonance that they used to. Can't use the Chinese, because even though it makes more sense it also carries that dreaded "racism" subtext that people are so afraid of.
Why don't we see games featuring the Cold War from the other perspective? Because these games are made in America, and the majority of Americans might feel uncomfortable slaughtering their own countrymen, even if they are just digital stand-ins. I once showed my Grandfather CoD: WaW, particularly the Japanese campaign. He served in the Pacific, and I wanted his opinion on how accurate they got it. He actually had to leave the room from being so shaken at watching even a recreation of something that had effected him so badly. Its a good thing I didn't tell him that the multiplayer let you play as the Japanese killing Americans, or he would have probably gotten upset.
TLDR Russians are a good enemy because they are still fresh in the public conciousness AS an enemy, while still carrying enough of the silly 80's Red Dawn vibe that no one actually hates them.
