You can use cron to schedule tasks.
Your crontab file could look something like this:
# Minute Hour Day of Month Month Day of Week Command
# (0-59) (0-23) (1-31) (1-12 or Jan-Dec) (0-6 or Sun-Sat)
0 1 * * * /usr/bin/python manage.py loaddata fixturename.json
(Or you can use @daily /usr/bin/python manage.py loaddata fixturename.json
to run at midnight every night)
See the webfaction documentation: http://docs.webfaction.com/software/general.html#scheduling-tasks-with-cron