AI is pretty dumb, it's better having a player as commander. For some odd reason, even if you have counter-measures they do not seem to work, there is however a counter-measures upgrade that the commander can purchase (bottom right of the tech tree).
You could try setting the AI accuracy in parameters to a lower setting, but you'll still be shot at by those super accurate tunguska's. Flying above 1000m also helps
You also have to recognise that some of the air vehicles do not come with counter-measures, it was only introduced with operation arrowhead, so some are still missing this simple feature.