a machine with that many parts flying in that many directions
It's really a function of the density and location of the zillions of moving parts. A small chopper is going to have the vast majority of its machinery packed into a relatively small space. That's why a random VC with a rusty SKS could pop a couple of rounds in the general direction of a Huey, get a good hit, and damage or disable something important. Although I suspect that the vast majority of those particular shots hit something relatively unimportant or just flew off into the wild blue yonder.
A jetliner is something vastly different. There are a whole bunch more moving parts, and it's a whole bunch bigger, but the distribution of important stuff is much wider, and a 747 can make a safe, albeit very exciting, emergency landing with a missing engine. There's a whole bunch of redundancy in a commercial jetliner, especially in the areas that would be easy to attack (multiple engines, multiple fuel tanks, various redundancies in control systems).
The pilot is, however, a big concern. Most crashes and infractions are pilot error, and a dead or incapacitated pilot is a much bigger concern than a bad pilot. If, and this is a BIG if, these "bring down a jetliner" idiots were actually concerned with planes falling out of the sky and not just wanting to disarm the peasants, they would be pushing for the simpler fix of armoring the cockpit against projectile threats. Armored glass and body panels are easy to come by, and there's a whole air force full of people who know how to do it. I'm not bidding on the contract, but compare the two options and you'll see which one is simpler, cheaper, easier, and just plain smart.