Do you send from filebeat to logstash or directly to elasticsearch? How many workers have you configured for output? Is loadbalancing enabled? Can you share your filebeat configs?
There are a many factors regarding filebeat performance. Just sending files to /dev/null on physical machine I was able to process like 95k eps. filebeat throughput depends on disk IO (unless files still buffered by OS caches) and downstream performance. E.g. if sending directly to elasticsearch indexing performance in elasticsearch. If sending to logstash throughput depends on processing time within logstash + performance even more downstream. This is due the outputs generating back-pressure if they can not keep up slowing down event generation in filebeat (as we don't want to drop any events).
somewhat related:
There's even a community beat collecting stats like in python script for storing in ES for example: https://github.com/urso/govarbeat