You do it the same way as you would a directory, but you specify the full path to the filename as the source. In your example:
rsync -avz --progress /var/www/public_html/.htaccess root@<remote-ip>:/var/www/public_html/
As mentioned in the comments: since -a includes recurse, one little typo can make it kick off a full directory tree transfer, so a more fool-proof approach might to just use -vz, or replace it with -lptgoD.