I was shocked that options like preserve and archive made no difference! This is a big deal and will catch people off guard.
Rsync include hidden files Solution:
You need to use something like:
rsync -Pha /source/dir/. /dest/dir
*Notice the "." at the end of the source directory.
cp -a still ignores them too, the solution is the same:
cp -a /source/directory/. /destination