Rsync is nice for remotely copying files over an encrypted connection. For a typical usage do:

rsync -ahvu --progress \
  --exclude 'folder/you/dont/want/to/copy' \
  --bwlimit=200 \
  -e ssh /source/directory/to/copy/* \
  user@remote.server.i.p:/path/to/where/you/want/to/put/it

Of course you can put this all on one line, but this shows how each thing works. The bwlimit limits bytes, not bits, so 200 really is about 1.8Mbps or so