OK, I'm going to give this a shot so maybe we can get you going! 😉
First off, does your site appear correctly in your default browser if you click the "Visit Site Now" button after iWeb has completed the "Publish to Folder" process?
Secondly, when you say you moved the file to the root in GoDaddy, does that actually mean to your account's "initial path"? By that I mean to the document storage path that is assigned to your account- for example if I am storing to my account's web space on "www.providername.com" and my user name is "user" and my account is on a server named "bigserver", I would set up my transfer program to log into the server as something like "ftp://bigserver.providername.com" and then specify that the "initial path" might then be "/user/docs".
Ok, I just realized that if you can see your site at all you probably have the files in the right directory, so just disregard that above-- I am just leaving it to verify your info. Oops!😱
At any rate, how you have your files stored in that space is really what is the important part. If you are publishing a single site to your storage space online, the end result from an iWeb generated site should actually only be two files showing in the initial path-
1. The "index.html" file created by iWeb when published to a folder on your hard drive
2. The folder (named "Whatever_you_named_your_site") which contains all the other files that iWeb published.
So let's start off with this for this round- is this what you see in your GoDaddy directory- an index file and a single folder?