I am sorry if that does not make any sense. So, when I publish the entire site--that piece of code, which I am understanding as the iframe, is being removed.
It makes sense. Everything is correct. However if you use iWeb'08 or iWeb '09 I would recommend you to add the iFrame code
<center><iframe src="http://www.thehoosierhysteric.com/comments/Blog.html" style="width:700px; height:500px; border-width:0px; border-color:#990033; border-style:solid;" scrolling="auto" ></iframe></center>
in an HTML Snippet in iWeb itself instead of adding the code to the page after you publish it. This way the code would be there even if hitting Publish Entire Site.