Yes, this is reasonably safe. People do this all the time, and they tend to be people who are sensitive to network security issues.
iperf3 is a rewrite of the original iperf software and has received more scrutiny then the original package, and iperf3 was created at a time when network security really does matter. The iperf3 developers do fix bugs and I believe Fedora/EPEL just released a 3.x update a month ago.
That said, all software has bugs and public servers will get attacked from time to time. Standard security practices should be used on your iperf server. Patch, firewall, consider firewalling off unnecessary ports from public networks, network monitoring, etc. I used the packages from EPEL because I know they have been tested by the EPEL community.
Try to avoid running network daemons as root. On CentOS 6 I believe that the RPM creates an iperf user and listens on a non-privileged ports. You could try running this service in a chrooted jail, or a Linux or docker container if you are feeling particularly adventurous.
Disclaimer: iperf3 is maintained by my colleagues at ESnet / Lawrence Berkeley National Laboratory. I can assure you these folks are very security minded. Computer defense is very necessary at the National Laboratories.
