I don't know NetBeans very well, so don't know of any workaround for the naming.
You can just name the file "package.html" and it will do the same thing. The drawback is that it won't allow for package annotations -- it can still have javadoc tags, though.
http://java.sun.com/j2se/1.5.0/docs/tooldocs/windows/javadoc.html#packagecomment