I asked this on Wars and they said you have to use high powered weapons, like mounted guns and the Gauss. They said even the sniper isn't enough, though I haven't tried this out yet.
I was taking out turrets on Mesa with my heli, and I got sniped right out of it with a DSG1. I've also been sniped out of it with a Gauss and other heli/VTOL guns.
Me and a friend tested whether you could snipe someone out of a VTOL. It's impossible. I let him sit there and the Gauss rifle and DSG1 bounced off (heavy caliber weapons can still kill you though)
There was one time when I bought a heli, as soon as I got in and flew up about 50 feet, there was a VTOL shooting everything it had at me, my first shot was lucky enough to go right through the glass of the VTOL and HEADSHOT the pilot. Oh man that was awesome