This is a very interesting question. I think the answer would depend on what you are specifically writing about. For instance, many of Tom Clancy’s novels had to do with the Cold War, therefore using Russians as his villains made sense. But if you are using Russians as your villains just for the sake of using Russians, I believe that it can lead people to have a very stereotypical view of them and can actually be detrimental to relations with the people in the country. Just as not all Italians are mafioso, not all Russians are spies.
I do not believe there are any politically safe countries. This can lead to hatred and distrust, which are unfair assessments of entire countries. If possible, the safest bet is to create a completely fictional world. If this isn’t a possibility, then my suggestion would be to spread it out a bit among all countries. Show a balance. Evil exists everywhere. All you have to do is turn on the nightly news and you will find that the world is not short on villains in every corner of the world.