Apple - How do I get rEFInd working with OS X 10.11 El Capitan?

You must disable System Integrity Projection.

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

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

I know this is an old question, but I just had to go through this issue when attempting to install rEFInd on a 2015 MBP. When trying to install by running ./refind-install in the terminal, I kept getting a message telling me that system integrity protection was enabled, and I could not do an install without rebooting into the recovery volume. The solution without disabling system integrity protection (it's probably there for a good reason):

1. In terminal, type cd ~/Downloads
2. Download the current install file with curl -s -L https://sourceforge.net/projects/refind/files/0.10.3/refind-bin-0.10.3.zip
3. unzip refind-bin-0.10.3.zip
4. Reboot, holding down cmd + r when the chime sounds
5. Open utilities -> Terminal
6. Your hard drive is no longer accessible at / since your on a different partition. Instead, it's now under /Volumes/{name of your hard drive}. If you don't already know what it's called (default is 'Macintosh\ HD'), type cd /Volumes, then ls to see it listed there.
7. Type cd /Volumes/{name of your hard drive}/Users/{your username}/Downloads. For example, mine is cd /Volumes/Macintosh\ HD/Users/Ayden/Downloads. Remember to escape all spaces in directory or filenames with '\ ', and use tab for autocompletion.
8. Type ./refind-install --root /Volumes/{Your hard drive} --yes. You should get a successful completion notice.
9. Reboot. You should see rEFInd. To see the default boot manager, press the option key while booting.

Note: to see more install options type vim refind-install while in the ~/Downloads/refind-bin-0.10.3 directory. They are listed at the top. To quit vim, type :q.

With the release of rEFInd 0.10.0, there's no official rEFInd documentation on this issue:

http://www.rodsbooks.com/refind/sip.html

That version's installation script (now called refind-install) also runs from the Recovery HD, and rEFInd itself can manage SIP settings, which give two more options for how to work around the issue.