I'd hazard a guess that most people who don't read what the uninstaller says it's about to do won't have read the readme or the wiki.
It's not uncommon for an application to delete the folder it was installed to, although most that do (including LFS) ask you first.
If the user doesn't click through the installer and goes out of their way to choose a non-default install location, doesn't notice that it's being installed to the root of Program Files, then doesn't bother reading what the uninstaller says it's going to do - even though there's a check box which is always a warning that it's about to do something you might not want it to - then quite frankly it is user error if the directory gets hosed.
Now, here's a real example of programmer error:
The uninstaller for Test Drive Unlimited deletes every file (but thankfully not folder) it has system permissions for in the root of C:\. One of those files is boot.ini, without which, many windows installations can't boot, rendering the computer unusable.
The really sad thing? They knew about this problem in the Beta, didn't fix it for release and didn't tell anyone about it.