This is one thing where I can easily say: What the fuck? I still remember the first time I used Linux on Mandrake and wondered what the hell all these three letter directories are. usr, bin, etc, dev, I still don't know what some of them do and ignore the conventions for other ones. Maybe on a server, or back 30-40 years ago when UNIX was king this layout was good, but for a desktop with one or two users it's more or less pointless. I'd have to say two of these folders make logical sense: home and usr (although usr could be named something a little more explanatory). Maybe tmp too. The rest of them (as far as I know, from my limited knowledge of the system underlying the pleasure that is Ubuntu) are generally system related and should probably go into a folder called system. This would leave us with 3, maybe 4 folders in the root directory: home (let's call this one users), usr (let's call this one programs), system and tmp. We now are left with Mac/Windows style folders! At least somebody gets it.
Unfortunately among the Linux crowd this directory layout has complete market penetration. Everybody uses it and probably all (or close to all) package management systems and autotools makefiles install things in this layout. This has about as much chance changing as Microsoft going out of business.