Of course, it also has disadvantages. A major advantage of embedding your SWF within an HTML document is the auto-detect Flash script that can be used. Don't just assume your user has Flash.
Some people are truly behind when it comes to technology.
Publishing your Flash Movie from Flash itself and specifying that you want an HTML page created will automatically add a Flash detect script and ensure everyone can see your site. This is a good thing. Another advantage is control of window size and placement on the HTML page. This can be accomplished using a little JavaScript that Dreamweaver or GoLive will write for you all you do is specify what size you want. It's simple and it ensures that you have total control of what the end-user sees of your movie.