Since every file is rewritten to the folder, modification dates are useless for use with an FTP program that supports syncing.
But if you have a webhost or server that you have shell access to, and the host runs rsync (most unix-based hosts should have rsync installed), then you can use checksums to only send files that are different. All you need to do is use rsync with the -c option. If you are removing files, you may also want to add the --delete option. For example:
rsync -avc Sites/mysite/ username@webhost.com:webroot/
I still have not found a way to convince iWeb to only output the changed files to the folder, but this at least gets you out of numerous unnecessary uploads.

