One day our society will probably get so pathetically politically correct that there will actually be an Anti-Nazi Defamation League protesting the depiction of its political ideology in games or movies. ><'
Still, I don't even really think of it as killing Nazis. Maybe because I don't see any difference between the average (key word being average) soldier on any side of a conflict. They're all just people being sent to fight by the ruling class of their homeland, regardless of whether they share the same political ideals. [/overly political comment]
Seriously, though, I think the only time the term 'Nazi' entered my mind while playing CoD5 was in the Nazi Zombie mode, and even then I was more focused on the zombie part. They could be replaced with any generic enemy combatant and the experience would be the same for me. I guess we're all just desensitised to Nazis, the same way we are to robots and zombies and 'terrorists'. Game developers go with them because they require the least thought on our part, by which I mean we're more likely to instantly accept them as the enemy without questioning their motives, right?