Operation Not Permitted when on root - El Capitan (rootless disabled)

Question

Nvm. For anyone else having this problem you need to reboot your mac and press ⌘+R when booting up. Then go into Utilities > Terminal and type the following commands:

csrutil disable
reboot 

This is a result of System Integrity Protection. More info here.

EDIT

If you know what you are doing and are used to running Linux, you should use the above solution as many of the SIP restrictions are a complete pain in the ass.

However, if you are a tinkerer/noob/"poweruser" and don't know what you are doing, this can be very dangerous and you are better off using the answer below.

Correct solution is to copy or install to /usr/local/bin not /usr/bin.This is due to System Integrity Protection (SIP). SIP makes /usr/bin read-only but leaves /usr/local as read-write.

SIP should not be disabled as stated in the answer above because it adds another layer of protection against malware gaining root access. Here is a complete explanation of what SIP does and why it is useful.

As suggested in this answer one should not disable SIP (rootless mode) "It is not recommended to disable rootless mode! The best practice is to install custom stuff to "/usr/local" only."

If you want to take control of /usr/bin/

You will need to reboot your system:

Right after the boot sound, Hold down Command-R to boot into the Recovery System

Click the Utilities menu and select Terminal

Type csrutil disable and press return

Click the  menu and select Restart

Once you have committed your changes, make sure to re-enable SIP! It does a lot to protect your system. (Same steps as above except type: csrutil enable)