I'm new to Axure, so maybe this wasn't true when this was posted, but it works for me in version 5. I create a page in the prototype called [filename]_start. This can either contain links to various parts of the prototype or it can be an empty page that just redirects to the proper starting point.
When Axure generates the prototype, this page replaces the standard [filename]_start.html file that Axure launches when it's done, which means when the browser opens you get the page you want instead of the standard frameset.
Creating a duplicate of this page called "index" will replace the index.html file as well, which should allow you to share the directory with users without having to worry about specifying "home.html" as the start page.
Because the pages are part of the Axure file, they'll be regenerated each time the prototype is.