Airlines are hypersensitive to weight since that affects range and fuel costs. The action that American Airlines took to remove complementary magazines from their flights saved millions a year in fuel costs.
In Air Force One's case - they probably have some active countermeasures (flares) and some electronic countermeasures (jamming) built in, but that's about it. Probably useless against a foreign state's advanced SAM capabilities. Much of the extra weight capabilities are most likely taken up by communications equipment to provide the President and staff command authority. Minus some rudimentary capabilities for low-end SAMs, Air Force One is probably just as vulnerable to being shot down as your average cargo airliner.
https://en.wikipedia.org/wiki/El_Al#Onboard_missile_defense_...
https://en.wikipedia.org/wiki/Boeing_VC-25
>All wiring is covered with heavy shielding for protection from a nuclear electromagnetic pulse in the event of a nuclear attack. The aircraft also has electronic countermeasures (ECMs) to jam enemy radar, flares to avoid heat-seeking missiles, and chaff to avoid radar-guided missiles
How much could Boeing, for example, modify one of their civilian airframes to support active countermeasures and make it capable of withstanding more stressful maneuvers without altering the outside too much? Quite a lot, I would think.