It's kinda funny that the greatest weapons technology supplier in the world and inventor of the Iron Man suit has no defense mechanisms at his house that would shoot down armed helicopters.
The helicopters are posing as News choppers
Stark probably thought they were paparazzi
This scene actually reminds me of the scene where Gary Busey shoots Danny Glover's former friend and source from a helicopter in Lethal Weapon, written by Shane Black. Admittedly, it wouldn't have occurred to me but for the Black connection.