It wasn't an unprecedented decision. Mount Weather in Virginia (see http://en.wikipedia.org/wiki/Mount_Weather_Emergency_Operati...) was an even bigger project designed to house and protect the executive branch, but it was compromised through sheer bad luck when in 1974 a TWA flight happened to crash into it. Reporters came to report on the crash and were surprised to find this huge, massively secure, fenced-off Federal installation in the middle of nowhere.
Mount Weather wasn't shut down after that, but its role as a key relocation point was scaled back considerably. The problem with Mount Weather after 1974 was the same problem as the Greenbrier bunker had after 1992 -- the entire value of a facility like that is dependent on the Soviets not knowing it exists, because hydrogen bombs are so powerful that it's pretty much impossible to build anything that can survive a direct hit. The only way facilities like the Greenbrier, or Mount Weather, or even Cheyenne Mountain could hope to survive in a full-out nuclear war would be if they were secret enough so that the enemy wouldn't target them directly.
Thankfully the prospects of full-out nuclear war aren't as bad as they used to be, so the investment in most of these facilities isn't totally wasted; many government leaders were relocated to Mount Weather on 9/11, for instance, when it wasn't clear if more terrorist attacks were imminent, and Dick Cheney is said to have worked for a time in the days after 9/11 out of Raven Rock. Neither facility would survive a direct hit from an ICBM, but when your enemies don't have ICBMs they're pretty much as secure as you can get.
Mount Weather wasn't shut down after that, but its role as a key relocation point was scaled back considerably. The problem with Mount Weather after 1974 was the same problem as the Greenbrier bunker had after 1992 -- the entire value of a facility like that is dependent on the Soviets not knowing it exists, because hydrogen bombs are so powerful that it's pretty much impossible to build anything that can survive a direct hit. The only way facilities like the Greenbrier, or Mount Weather, or even Cheyenne Mountain could hope to survive in a full-out nuclear war would be if they were secret enough so that the enemy wouldn't target them directly.
Thankfully the prospects of full-out nuclear war aren't as bad as they used to be, so the investment in most of these facilities isn't totally wasted; many government leaders were relocated to Mount Weather on 9/11, for instance, when it wasn't clear if more terrorist attacks were imminent, and Dick Cheney is said to have worked for a time in the days after 9/11 out of Raven Rock. Neither facility would survive a direct hit from an ICBM, but when your enemies don't have ICBMs they're pretty much as secure as you can get.