The point is, the Mac is not as intuitive as it was with OS/9. Building a layered system on top of Unix means you will get exposed to Unix from time to time. Usually when you don't expect it.
Blaming the user for removing a directory that took 4 hours to recover from, well, that can happen with ANY Unix system. It's why we depend on multiple user accounts with different priviledges, "hidden files" are a Mac Finder thing that are a form of "security through obscurity", not the best practice anyway.
Apple does its best to provide training wheels, but not everything works 100% of the time. User accounts should not have admin priviledges by default. And applications (pay attention here, Adobe and Yahoo) should not require ROOT/Admin priviledges to be installed on a Unix system designed for end-users. If I want to run Yahoo Messengers, that's a pretty basic browser style app, no priviledged ports are needed, so no admin priviledges should be needed to install into my home directory.
More people have multiple computers, and vendors aren't doing adequate testing with ACTUAL platforms their customers use (considering all the "use cases", as some would say).
Whether the /usr directory is "hidden" or not, it shouldn't be able to be deleted casually, even by a determined user. Files in /usr should be marked as read-only, and if the NAS appliance doesn't support or honor file permissions, it fails some pretty fundamental tests.
I have 26 years experience w/ Unix, 23 with Macs. I use OS X every day, and I still run into "issues" from time to time. But I'm generally happy that I have a Unix platform with the Applications that I need to run.
My other machines run Linux, and it's not always perfect, but it keeps my mother happy that she can e-mail and browse the web without having to be a Windows system administrator. She doesn't like to monkey around with any computer stuff, and the last thing I want to do is come home to manage yet another Windows system.
And They Said the Mac Was Intuitive