Please take the below with a grain of salt. This solution appears to work, but I haven't extensively test it.
I just installed this add-on yesterday and ran into the same question. It turns out that the scripted input, nessus2splunk.py, parses the plugin_output tag in the source xml, but doesn't write it to the munged file that is sent to $SPLUNK_HOME/var/spool. The simple answer seems to be to edit the python script, $SPLUNK_HOME/etc/apps/Splunk_TA_nessus/bin/nessus2splunk.py, and add the single line:
('plugin_output', 'Data', str),
just below line 339 making sure the indentation (using spaces not tabs) matches up with the surrounding lines. When you're done, a simple diff of the revised file with the original file gives: