The documentation in Presenter is a little misleading in that it does in fact create a swf file called "viewer.swf" and "viewer-lite.swf" and you can in fact load those swf files independently on a web page, but what it doesn't tell you is that those two swf files pull data from the rest of the normal Presenter output into them to render the content. So yes they are swf files, but no they are not a flat swf file that contains all the content, it's merely a container that the data loads into. I hope that makes sense.
What you could try doing is using one of the open source (free) solutions that convert pdf documents into swf files.
http://pdfmenot.com/ is a good web based one to try. Here is a tutorial on how to use it, http://www.labnol.org/internet/tools/convert-pdf-flash-pdfmenote-online-pdf-to-swf-converter/2280/
You could also try http://www.swftools.org. This is a more involved method and uses command line entries, so it's a little daunting, but here is a short step by step, http://www.ehow.com/how_4844986_convert-pdf-swf.html
Another option would be http://pdfzilla.com/. This is not free but seems to be a much easier solution.
I hope this helps.