There are many ways to update your path. Jun1st answer works great. Another method is to augment your .bash_profile to have:
export PATH="/usr/local/bin:/usr/local/sbin:~/bin:$PATH"
The line above places /usr/local/bin and /usr/local/sbin in front of your $PATH. Once you source your .bash_profile or start a new terminal you can verify your path by echo'ing it out.
$ echo $PATH
/usr/local/bin:/usr/local/sbin:/Users/<your account>/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
Once satisfied with the result running $ brew doctor again should no longer produce your error.
This blog post helped me out in resolving issues I ran into. http://moncefbelyamani.com/how-to-install-xcode-homebrew-git-rvm-ruby-on-mac/