Update (12 Feb 2016):
I finally installed El Capitan and can now confirm that Ondřej Čertík's answer is correct. I strongly recommend installing the command line developer tools instead of disabling SIP.
As Ondřej noted, simply installing Xcode will not install all of the command line developer tools. You must execute
xcode-select --install in Terminal.
Original post (5 Dec 2015):
Write access to /System, /bin, /sbin, /usr, /etc, /tmp and /var has been disabled by default in El Capitan, even for root. This is due to the new Security Integrity Protection feature.
To disable SIP, boot into recovery mode and execute the command
csrutil disable in Terminal.
Disclaimer: I have not tested this myself since I have not yet upgraded to El Capitan.