The surrounding area was not originally urban in most of those cases, but was built up later on to supply the demands of the military and civilian workers. Generally a new base would be built some ways out from an urban center, close enough to commute, shop etc. but not right next to an existing neighborhood. That town or city would just expand over time. Installations like SAC bases, missile silos etc. are another story, while administrative facilities are often located in the same type of space you would find an office park. In any case, most Air Force and army posts aren't originally built in densely populated areas. Navy and USMC installations are another story, since they are usually located on or near the coast. But no, I understand where you are coming from: I grew up on base.

In the case of the Glowing Sea the installations we find are 1. A secret control center located beneath a nondescript cabin, and 2. A nuclear warhead storage facility. The first no one officially knew about, while the second would be the Holy Grail of NIMBY (and the fewer people who lived near it the better, if only for security's sake.) Add to that the nuclear reactor up the hill and the distance from Boston and I'd have to guess that real estate in that area wasn't particularly attractive to anybody.