On my Iweb page I have comments allowed on my blog. Yet no one can post comments. It comes back with an error message. I have my site linked through Go Daddy could this be the problem?
^Yes, I believe you are correct, by using dotmac the database is set up automatically to work with the blog, but when publishing to a folder and uploading to your own FTP storage, there won't be such database, and Apple doesn't give you the option to configure iWeb to work with one.
You could try using the Wordpress blogging software which works with MySQL and enables you to have comments, it's free.