Once you publish your iWeb site to a folder you should just be able to dump that folder on your web server via FTP.
You don't need anything fancy to "export" your site from iWeb. Just select "File" then "Publish to a folder" and pick a location. This will give you a folder with your entire website inside (in subfolders). This is everything you need to send to your webserver.
You should be able to use any FTP to get it to your webserver. I use Fetch when I have to FTP stuff (though I use .Mac for my actual website).
You're probably having an issue with either uploading to the right directory on your host / virtual webserver (if you're on a virtual webserver, you might need to upload to a SUBfolder on your server like /yourusername08765489/uploadhere/ ,not the root).
or...
with uploading your published set of folders from the correct starting point (I believe iWeb puts your website IN a folder like "Documents:Websites:web:site", and you're supposed to upload the folder located one level down (site), not the first level (web), IIRC.
However, those are just guesses because you didn't give us much to go on in your OP. What happens when you try to access your site in a browser? Do you see something, but not what you expected? Is it returning a 404 error?Are there any error messages during transfer? Are you trying to access your site using a domain name, or are you going to it via an IP address? Is your name setup OK (if you're using a domain name)... has it been working previously?