rsync not actually copying files

Solution 1:

You could simplify your command to

rsync -az --stats 69.46.18.236:/var/www/phrogz.net/public /var/www/phrogz.net/

or alternatively

rsync -az --stats 69.46.18.236:/var/www/phrogz.net/public/ /var/www/phrogz.net/public

As you see, rsync interprets differently a source with or without a trailing /.

Also, -a is equivalent to -rtplogD, (with respect to your command line, the -a also adds -o, preserve owner, -g, preserve group and -D, preserve devices and special files).

Finally, the --rsh option is redundant when the source or the destination is in the form host:/path, with a single :.