It doesn't train them how to use real computers, but that's not on the state standards so they don't care.
The reasons schools ate them up os because they're cheap and were the most readily available laptops during a shortage. I really doubt much else was on anyone's mind.
1. For a Linux user, you can already build such a system yourself quite trivially by getting an FTP account, mounting it locally with curlftpfs, and then using SVN or CVS on the mounted filesystem. From Windows or Mac, this FTP account could be accessed through built-in software.
2. It doesn't actually replace a USB drive. Most people I know e-mail files to themselves or host them somewhere online to be able to perform presentations, but they still carry a USB drive in case there are connectivity problems. This does not solve the connectivity issue.
Arguably, it really should be.