Well, it's actually $3.75 billion. And it's not one, but two aircraft, so that's 1.875 billion apiece. That's to ensure the executive branch can function in a military crisis while one of the planes is being service.
Deduct 375 million apiece for the airframe, and we're talking 1.5 billion dollars in customization for each aircraft, including aerial refueling capabilities, which on a two-off job is a craft job; no economies of scale. Add defense and countermeasure capabilities that Air Force is extremely close-lipped about. Is there a actual escape pod on Air Force One like in the movie? Well probably not, but I'm sure the idea was at least contemplated. However it's pretty certain that if someone locks onto AF1 with a targeting radar the aircraft will have options that a stock 747-8 doesn't.
Next outfit each one so it can function as a replacement for the West Wing and the Situation Room for up to two months -- that's a deducible requirement based on the known fact that the aircraft stores 2000 meals for 100 people. That means three-of-a-kind electronics and communications systems (one for each airframe and one for the actual White House).
Is 3.75 billion too much for that? Probably. But it's hard to think of any weapon development program since WW2 that is less extravagant.
By that standard 127 million for an orbital repair robot is an almost inconceivable bargain, even if you factor in a 5x cost overrun.