InDesign doesn't have a canned mechanism to make this easy.
So you'll need to export the PDFs to files on your local machine and then ftp those files elsewhere.
You can do so by invoking the command-line ftp client, or by using curl's ftp upload, or scripting Fetch, or any number of other solutions.
It probably depends on what you are most familiar with. I guess I would probably start with curl, if you don't have a preference.
(P.S. In English, we don't say "an FTP." It's "an FTP server" if you mean the destination to which you FTP files.)
Thanks - I think ; - )