rsync is very good at keeping directories in sync, and ssh is
de-facto standard for "generic" wire crypto; you can use them
both to sync local directory to say website root on a server:
rsync -Pav --delete-after --bwlimit=60 ~/website/ user@xxxxxxxxx:/www/web.si.te/html/
which would synchronize utilizing partial uploads when
neccessary, archival options (that is, file times and permissions
will be transferred and set too if possible), some nice verbosity
and using no more than 60 Kilobytes per second in bandwidth
(sparing the rest of DSL). The files absent in original will
be removed in destination after content sync finishes.