srothstein and a couple others hit on the key reason -- when development around a base starts causing problems for the military, either via complaints about noise or actual impingement on activities, the military starts considering moving missions, and eventually bases, and all the jobs and money that go with them. Why doesn't the military buy buffer zones? I believe it has in some cases, but looking at it strictly from the feds point of view, why should they? They will get all tangled up in court cases, eminent domain, etc -- let the city figure out all that stuff. BRAC showed people that bases actually can close -- and even ones that survive the BRAC, or get cherry-picked for special treatment (e.g. Brooks City-Base), can close as well, or be diminished so much through movement of missions that they might as well be gone. (The Air Force decided years ago to close Brooks, and for all practical purposes, they did.)
Even before BRAC, this went on. At Tinker AFB in Oklahoma City, the city bought out a subdivision that was being constructed just north of the base, which put it directly in line with the north-south runway. Was kind of interesting -- there were paved streets with no houses up there. While I was stationed there, one of the local mega-churches decided to build an even bigger building directly in line with the other runway that ran NW to SE -- according to the plans, the top of the spire would either intrude or be very close, I forget which, to the glide path for some aircraft. That church threw a fit when the church went to the city for its building permits (after it bought the land and made its plans), the USAF was asked to comment on it, said "bad idea," and the city balked on the permits. The church raised cane for months, accused the Air Force of all kinds of underhanded stuff. It was solved when a rich anonymous donor gave the church more land on the same street, but farther south, out of the path of runways.
So some some cities like to avoid all the drama and restrict the zoning around the bases. As long as they are in the zoning business, this makes sense to me, and if the locals want to vote for it, fine. Like srothstein I can't figure out people who move next to a military or civilian airport and then complain about the noise.
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