Plyxim's Easy iWeb Publisher 3.0.3 fixes that problem. The shareware ($7 donation requested) application makes it simple to publish to any web host. It's an ftp client that takes the local folder you've published your iWeb site to, compares it to the folder on your web server, and then uploads just the files that have changed.
I've found that Easy iWeb Publisher works much faster than most dedicated ftp clients when syncing iWeb files that have been changed, added, or deleted. Until Apple fixes iWeb '08 to make publishing easier for people who don't use MobileMe, this is a great way to work with your own hosting.