A colleague recently asked me if there was a way to save a publishing site as a template recently. I responded by informing them that the "Save site as template" link is on the Site Settings page under Look and Feel. He said it was not. After a quick investigation, I realized that it is in fact not there; see below...
Blank Team Site
Collaboration Portal (Publishing)
The easy solution that seemed to work, and I leave you with the caveat that I have not fully tested this solution, is to simply determine what page this link goes to on a Team site, namely savetmpl.aspx, and type that into the location bar of your publishing site. The "Save site as template" page then appears and you are able to save your publishing site as a template.
Blank Team Site
Collaboration Portal (Publishing)
I am not sure why they removed this link on the publishing enabled sites, but I am certain there must be a perfectly good reason; maybe there are some things that happen in a publishing site that you simply cannot store in a template. If anyone is aware of the reasons or has seen them documented somewhere, please do let me know.