Them choppers have a priority when they select targets. Quite naturally they will first take out the vehicles, and I don't know anything how to prevent it, other than the dotarget, dofire thing mentioned above.
As for the units on ground, there's no way that I know of to make them shoot the choppers with pistols and such. It's a build in thing called realism which is really annoying sometimes. The AI thinks "Oh well, I only have so small gun, there's no use for me to shoot that big old chopper with it."
It's the same as you'd order them to shoot a tank, they just won't do it because they can't make any damage anyways.