In El Capitan, you are not allowed to write to /usr/bin, but writing to /usr/local/bin is ok. By default, /usr/local/bin should also be in your path variable.
Had the same issue. Deleting and recreating the symlink has fixed the problem. Perhaps the current symlink is pointing to the wrong location after the upgrade.
sudo rm /usr/local/bin/subl
sudo ln -s /Applications/Sublime\ Text.app/Contents/SharedSupport/bin/subl /usr/local/bin/subl
Or Sublime Text 2 (from – @simen comment):
sudo rm /usr/local/bin/subl
sudo ln -s /Applications/Sublime\ Text\ 2.app/Contents/SharedSupport/bin/subl /usr/local/bin/subl