I honestly don't think there is an issue with allowing Instapaper content to get backed up to iCloud here. The analogy of a user created archive is a good one.
If people don't want the benefit of having their Instapaper content transfers across their devices automatically (and I do think this is a good feature) then they are free to disable iCloud backup for Instapaper in Settings.
That's not entirely true. You can disable iCloud syncing for individual Apple apps, but 3rd party apps are all-or-nothing. You can't disable iCloud syncing for a single 3rd party app.
(That's a serious question, BTW. I would check it myself but I can't upgrade to iOS5 until I figure out how to get Windows DEP to stop killing iTunes 10.5 every time I launch it.)
I didn't find that setting screen. Definitely didn't see that in Settings/iCloud. I wonder how you get to that... I only had a chance to briefly look at my roommate's 3GS on iOS 5; won't be on iOS 5 myself until my 4S arrives later today.
Weird. On my roommate's 3GS upgraded to iOS 5.0 (I've not upgraded mine yet as my 4S is arriving today), I did not see the screen shown in the screenshot linked in the post above in the Settings/iCloud section. There were toggles for all the Apple apps, but 3rd party apps seemed to only be able to be toggled all at once, with a toggle called "Applications and Documents" or something of the sort. How do you do it?
If people don't want the benefit of having their Instapaper content transfers across their devices automatically (and I do think this is a good feature) then they are free to disable iCloud backup for Instapaper in Settings.