Semantics: You want to get them right but sometimes they're just confusing.
Website document structure:
<body>
<header>
<div id="main">
<header> (not on every page)
<div id="content">
<footer> (not on every page)
<aside>
<footer>
Is it semantically correct to replace div#main with an article tag?
As per http://html5doctor.com/the-article-element/ that is a valid semantic way of coding. It is referred to as "A weblog-style <article>".
Depending on your structure you might be able to replace #content with an article as well.
Do not forget to include http://code.google.com/p/html5shiv/ and while you're at it if you serve your site over https also look into Protocol Relative Url (Google for it), so you don't have to detect the switch between http and https.