Why can I not sometimes hijack a helicopter, and instead hang beneath it getting ripped to shreds?

I think you need to be in front of the vehicle to perform a hijack for planes and helicopters. When you are in the bottom, try to move the joystick so you'll transfer on top or in the front. And yeah, you need to take down to co-pilot too if there is one.

Maybe this video will help

As you can see he go in front of the helicopter to do his hijack. Hope this helped!

When a helicopter is manned by two people, a gunner and a flyer, you must first take out the gunner before you are able to hijack the vehicle. To take him out, grapple on to the helicopter so that you hang from the bottom as usual, then move towards the front of the helicopter, causing your character to swing on to the front of the helicopter. From here, lean towards the gunner's side and kill him using whatever sidearm you want. You should now be able to hijack the helicopter.