How do I get rEFInd working with OS X 10.11 El Capitan?
You must disable System Integrity Projection. 


Restart the computer, while booting hold down Command-R to boot into
recovery mode.
Once booted, navigate to the “Utilities > Terminal” in the top menu bar.
Enter csrutil disable in the terminal window and hit the return key.
Restart the machine and System Integrity Protection will now be disabled.


source: http://mattjanik.ca/blog/2015/10/01/refind-on-el-capitan/