cp -r /source-folder /destination-folder

will not preserve permissions - you want to preverse permissions if backing up folder on a live server.

cp -a /source-folder /destination-folder

does the backup you want :)

using wildcard in a transfer ignores hidden files.

rsync -avz * /dest/folder

will ignore your .htaccess and any other hidden files, just copy the directory or use . within the directory, not * to transfer all.

rsync -avz . /dest/folder