That's the problem with the iPhone/iPod/iPad.
Apple seems intent on making the way you access them the same on Windows as on the Mac which seems to be giving us the lowest common denominator - the bloated, clunky, cross platform Carbon crap that is iTunes.
By not trying to make Windows users second class citizens, all they've done is also make Mac users second class citizens.
On the Mac they should be using AFP, Bonjour and SyncServices and NOT iTunes.... or as someone said earlier, just buy/clone DropBox or Ovi Files.
The iTunes file sharing kludge is ridiculous.
I can see both sides of the argument. For people who know computers and file systems, etc. I can see why we want the freedom. but to those who do not know much about them, then the itunes was is easier for them. They just drag it to the app they want. and when they sync. bingo it is on the ipad/pod/phone.
For the person who asked about backing up documents that are in apps, I think it does when you sync with itunes. my current phone usage shows 1.44 for apps, 53mb photos, 100mb music, 800mb other. Since I have no movies on my phone, I can only assume the other are my documents in stanza, air sharing, mobilestudio, and my library files for my bible software. The other tends to accumulate more mb's used as I bring books into Stanza. Also, I notice my harddrive space on my macbook does drop when I create something on my phone and sync to itunes.
So I am for the file sharing as it should make an easier way to drag and drop between my macbook and device.
Ok, off to write my next sermon on my iphone.