The Unix versions of VMD have an extra -webhelper command line flag which causes VMD not to be spawned in the background, so that it has time to read temporary files downloaded by the web browser. This command line flag is just slightly simpler to use than the chemical2vmd script, as it does not depend on having Perl installed, so may be more appropriate for some cases.
In the VMD installation directory ($VMDDIR/scripts/vmd/) there is a perl script called chemical2vmd which will create a VMD command file and execute VMD. Since VMD does not block the calling process, Netscape and other web browsers cannot directly call VMD, as they do not know when to delete the temporary file containing the molecule or other data. The chemical2vmd script starts VMD with the -e command line option which runs the saved VMD script or molecule file.
It is also possible to install the previous script in the global .mailcap file to make it accessible to everyone. You will have to consult the documentation for your web browser(s) to find out how.