I was having this same issue and fixed it with the following:
- I was also running Macports (Homebrew does not like this), so the first step was to move /opt/local to ~/macports
"sudo mv /opt/local ~/macports" per the "$ brew doctor" recommendation when it discovered macports config files. My guess is that this is what ultimately fixed the issue, but I also took further steps suggested in the post linked below.
- Manually forced generation of dot config file: $ dot -c
- Verified the the existence of the folder "/usr/local/lib/graphviz" and the config6 file.
http://www.graphviz.org/content/graphviz-os-x-mavericks-update-there-no-layout-engine-support-neato