Realistically, as more was learned about the effects of Nuclear war, as the bombs got bigger and more accurate, and the effects of radiation became more apparent, it became obvious that you really couldn't begin to protect every American without an expenditure that was totally infeasible. You couldn't really even protect our culture. You could protect a subset of the population though, if you could decide who those people were. But as a nation we didn't really have the stomach for it or the money.
But the fallout 3 world is not our world. For them, the bombs didn't apparently get bigger. The microelectronic age didn't happen so perhaps high accuracy didn't either. They had resource exhaustion happen much earlier than we might. They perfected practical portable fusion power, as well as energy weapons and robots (and power armor). They had YEARS of war between Europe and the Middle East as well as US vs. China where nuclear war could break out any time. I read somewhere that the "real" FO3 gov plan was to build rockets to some other planet, but the vault program does seem a lot more likely under these circumstances. Of course the "experimental" nature of the vaults shows that they were really not thinking ahead to use the vaults as backups to save as many people as possible. If they had been the experiments would have been suspended. Of course the war happened fast, but the overseers could still have stopped some of the more destructive experiments.
I don't notice many "personal" fallout shelters in the FO3 towns (Springdale has 1 I think that is later used for the radioactive water snake oil salesmen). So that is similar to our world. The buildings are much more "bunker like" than our world though so the architects seemed to be trying to protect against bomb effects a bit more than ours did.
On the whole I think the vault program is plausible in FO3 despite the lack of traction that community shelters had in our world.