> I don't see what this has to do with real-life urbanization, either.
The problem on the server in this article isn't "urbanization", it's a failure to create appropriate infrastructure for the task at hand.
The repeated question and answer pair of "where are the trees?" "Try the edge of town" suggest limited Minecraft-life experience, and probably limited life experience in general. Had they simply set up a policy of "every time you harvest a tree, replant two saplings" there soon would have been a large enough tree farm to satisfy all 50 players, as trees in Minecraft grow quite fast. Had players built deep mining tunnels and used any of the common mining techniques [0], they'd have had all the cobblestone (and various other ores) they wanted, without stepping on each others' toes. Instead, they were so short on resources that they felt it necessary, when fleeing their initial city, to salvage torches -- which are quite easy to create in bulk.
For comparison, my mostly adult gaming clan runs an invite-only Minecraft server. We've built up a ton of infrastructure -- a five-acre ranch [1], a greenhouse, mushroom farms, tree farms, strip mines, and monster farms, so we have easy access to virtually every type of resource. Everything is interconnected via rail lines or portals, so material transport is not an issue. If someone decides they'll need a lot of a particular type of material, we set up a system to allow us to harvest that material in large quantities. This allows us to build ambitious projects fairly quickly. This is typical of well-run Minecraft servers.
[0] http://www.minecraftwiki.net/wiki/Tutorials/Mining_Technique...
[1] http://ripminecraft.blogspot.com/2011/04/tomcat-ranch.html