I whipped up some rules for vehicle trashing.
You can just leave things as they are. Don't have people with tac missiles take on PCs in an ATV. Vehicles are to take you from point A to point C (point B is where you stick in things like a rockslide or an amorous encounter between a dinosauroid and your ATV.)
Give the group a roll to avoid destruction of their ride similar to avoiding mishaps with a DM based on the threat level. A Scout with a body pistol isn't going to bother an AFV much and not for long if you have a gunner. So, an ATV that has to throw +4 to avoid mishap might take a -1 for each 3D the attacking weapon does or -1 per die if you like blowing ATVs up.
The CT system is one where armor affects hit probability. I'm going to assume a plain vanilla civilian vehicle has a skin equal to mesh. It has some value against bullets but isn't designed for defense. Penetrating the armor is not the whole story because you have to hit something important to affect the vehicle. That sounds like cover to me. That affords a -4 to be hit for humans and we can assume most vehicles have a volume of important stuff equal to a human in size. So the mesh is further modified by -4 max. Smaller or more exposed vehicles will have a smaller modifier. Helicopters and airplanes are pretty fragile, they might rate mesh -1, hovercraft -2, air rafts, ground cars -3 and the huge ATV types the full -4. Note that while hitting a 5 meter ATV is easier than hitting a sportscar the ATV is way less likely to notice you and your autopistol (except for that bump. Did you feel that?) Automatic weapons roll for additional hits normally.
People in the vehicle that are partially exposed would get -1 to be hit at Medium, -2 at long and -4 at very long. Like evading. People in an open topped vehicle like an air raft only receive a -1 to be hit at long and -2 at very long range. A vehicle passenger or crewman just hanging out doesn't get this bonus. Keep your head down. Passengers using gun ports to attack are -4 to be hit. That's serious cover.
Ruggedized vehicles like the ATV would have a base armor class of cloth. Paramilitary vehicles like the AFV or GCarrier might have combat environment or combat armor equivalent. If you want to talk heavier armor get Striker. Mr. Chadwick does a way better job than I do.
A hit to a vehicle can use the small craft damage table from Book 2. Generally a hit disables a system.A drive hit means your ride is over. High performance vehicles like the speeder or ground car could take two or three drive hits with speed being reduced by 25%, 50%, 75%.
Small arms that hit a vehicle have a 1 in 6 chance of damaging a system for each die of damage they cause, so 3 in 6 for most firearms. Optionally just give the vehicle a hit whenever the damage inflicted adds to six. So if you manage to hit the AFV with you body pistol you have a 2 in 6 chance for it to notice.
Ship lasers will do 1D of hits to a vehicle. Missiles (ship mounted or tac) will do 2D. Optionally apply the hits all to one system. A vehicle can take hull hits equal to its tonnage before catching fire, exploding or just being blown into confetti. Throw +10 to bail out of a vehicle, +appropriate skill, +1 if Dex is 9+. Success means you get out mildly singed or bruised and manage to grab your gear. If the roll is '7' or less you take 1-6D of damage and get out with just the armor on your back . An '8' or '9' means you take 1-3D and grab a sidearm or other small item.
Weapons on a vehicle can be fired at speed bumps errr people. The human targets get a -1 to be hit, -2 from turreted weapons.
Vehicles can evade like characters. This only works vs. vehicular and similar weapons.