Okay - you obviously like government planning as you keep defending it as some kind of neutral operation devoid of politics. Here is a really good book to read if you are so inclined - http://store.cato.org/books/best-laid-plans-how-government-planning-harms-quality-life-pocketbook-future-hardback.
While some government planning is good, think Planning & Zoning, for the most part it is initial planning to make maintenance planning in the future easier.
Think about a building. You want it to have electricity, water, and sewage. But these are not independent operations, they connect to larger systems. This saves everybody money, time, effort, and keeps the value of the area. Then, if the building is in the middle of nowhere, it is going to be a pain for whoever lives there to buy groceries, gasoline, and whatever else they want.
I also agree that if an area is already built up, you should not interfere with those who live there. But in the case of Israel, this was empty desert. No infrastructure, roads, agriculture, business, industry, or any appreciable local government.
So their overall prerogative was to build interconnected settlements, at least as far as infrastructure goes, that make it as easy as possible for the Israelis to dominate the area, mutually support each other, and have what they need to develop.
Everything else in there, you added, but is not an inherent part of doing this. “Oh, oh! Having paved roads will make it easier for government tanks to roll in and kill everyone!”
Well, yes, but the vast majority of the idea of paved roads is not for that purpose. In fact that almost never happens.
“But it could, so we should never have paved roads!” Which just sounds silly.