Ok you need to run bin/logstash -f /path/to/logstash-simple.conf. The bin/logstash part is simply a convention or short hand for "invoke the logstash binary". If you saved the logstash directory under /bin, i suspect that your invocation should be /bin/logstash-2.0.0.1/bin/logstash -f /path/to/logstash-simple.conf. To confirm:
What is your absolute path to the logstash binary? and to logstash-simple.conf?