The System Integrity Protection (vulgo “rootless”) feature of OS X El Capitan protects critical filesystem areas from root user modification attempts.
SIP is part of a defense in depth approach to securing OS X. Once an attacker has root privileges on 10.10 and before, they can change any aspect of the system. SIP locks down these critical areas in a way that not even root user can modify. This causes some headaches for programs and scripts that depend upon root access and don't live well in a sandboxed app environment. This causes great rejoicing from people who clean up relative's computers that are infected with malware, adware, spyware and other bad acting software.