I've just sent this as a feature request to iWeb. It currently CANNOT load straight into the public_html folder.
it ALWAYS creates a folder with the same name as your site name that will sit under your server's root folder.
So what I do to prevent having my website go from example.com to example.com/example in the URL, I publish to a local folder and then drag the contents using CyberDuck (free).
Or, you could try calling your site public_html and see if that works at "tricking" the root into accepting that the iWeb directory site folder name (now called public_html) over rights the root folder on the server, so that your site sits in the root. I know it's a terrible name sitting on your iweb folder, but no one else will see it if it works.
Other than that, I've written to Mac about it and we'll see what 2010 brings.