It\'s really quite annoying as they are not part of the project.
I know this is really old, but maybe someone else will be helped with my reply.
I found the solution here: http://www.meadow.se/wordpress/?p=137
Basically, add these lines to the bottom of your web deployment project file above the tab.
Just put your folder or file in there too and it will not be copied over.
The Visual Studio Web Deployment addin lets you exclude folders and more. VS2005 VS2008
Also a decent writeup on the Web Deployment addin