Sure the site assistant is just a wizard tool. You can create your own custom PHP pages.
With Custom Web Publishing (CWP), you can pull your data from your database and use it in any custom coded Web page. Getting FMP to export it's data in XML allows you to use any code you want, but there are several PHP classes available to easily work with FMP XML exports. Google "FileMaker PHP XML" and you'll get tons of resources. The issue is setting up the server... which is my problem right now...