How can I restore the permissions of my "/usr" folder?

Do you have a backup?

If not, you should be able to fix the permissions by booting into Single User Mode. Hold CmdS while rebooting, and in the prompt, enter mount -uw /.

Then try running:

chmod u+r /usr

which should give the owner read permissions again. You can, of course, do that recursively by calling chmod -R u+r /usr, depending on what exactly you did to screw up your permissions.

If you also changed the owner, you can set it back to root:wheel for /usr and its subfolders, except for /usr/local, which should probably be username:admin (where username is your admin user's name).

Once you're done, type reboot.