How to remove Apple System Apps
@grgarside: El Capitan and later won't let you just rm the default apps, they're protected. – grgarside 11 mins ago 


That's because of El Capitan's System Integrity Protection System (SIPS), which prevents even Root from making (potentially harmful) changes to the system. A fine idea in principle, apart from the fact that it stops you doing a lot of things whose "integrity" to the system is spurious –such as changing the speech bubble colour in Messages, or deleting pointless Apple apps you never use.

You can disable SIPS by booting into Recovery (Hold down Command+R at startup) and then using Utilities > Terminal issue the following command:

csrutil disable


and then rebooting.

Normal God-like power will now be restored to root and you're free to delete Apple bloatware.  To re-enable SIPS, the corresponding command from recovery is:

csrutil enable


However - and it's a big "However!" - with SIPS re-enabled again, OSX will silently restore any system apps you deleted. I found this out when I disabled SIPS, removed iTunes, re-enabled SIPS and found iTunes back in my Applications folder a few days later.