If I recall correctly, you can still view it under the Terminal. For normal end users, it's not necessary to see this folder, but it's there if you do a "cd /" in the Terminal. Why do you need to see it under the Finder?
There really is no need for everyday users to see system directories like /usr and others. It just asks for more problems when they decide that it doesn't belong there and move it to another location. For advanced users that need to access those system directories, they will know how to get to them.
Now since it IS your computer, you can do whatever you want with it. As for how this is done, I'm not quite sure. I've actually never researched it since I haven't had the need to see the /usr folder unless I'm using the Terminal for whatever reason...but that's me.
tell application "System Events" to set visible of (choose folder with invisibles) to false
tell application "Finder" to quit
delay 2
tell application "Finder" to activate
Paste the above lines into an "/Applications" > "AppleScript" > "Script Editor.app" document and click "Run". Substitute "true" for "false" to reverse the change.
You can add a period before a file to make it invisible, but that's probably not a good idea, as it would change the filename. You might want to try a program that can make files invisible, like this: http://www.ragesw.com/if_faq.php
If I recall correctly, you can still view it under the Terminal. For normal end users, it's not necessary to see this folder, but it's there if you do a "cd /" in the Terminal. Why do you need to see it under the Finder?