we configured the cloud images to run the ctlscript on startup, so if you don't want to start one application you will have to rename the ctl.sh script of the application. I mean, if you don't want to start Apache you will have to rename the file at /opt/bitnami/apache2/scripts/ctl.sh to ctl.sh.backup and Apache won't start the next time that you reboot the machine.
If you want to start Apache once the server has been started, you will have to run the following command.
sudo /opt/bitnami/apache2/scripts/ctl.sh.backup start
Finally, if you want to start Apache on startup again, you will have to rename the file from ctl.sh.backup to ctl.sh
Let us know if you have any more questions!