I tried using terminal with
su, while I do
rm -rf to Photos.app, Chess.app, Mail.app, DVD Player.app, iBooks.app, but it said Operation not permitted.
How can I delete these apps?
(OS X version is 10.11.1)
Being OS X El Capitan (10.11) has, from what I understand, the same System Integrity Protection as the current version, macOS High Sierra (10.13), I think the steps are the same. You can delete at least some of the applications. I haven't tried them all but I deleted Maps, Chess and DVD Player.
First, you need to boot into Recovery Mode. Hold
CMD + R after the boot chime. From there you can go into the Terminal and type
csrutil disable. Reboot. This disables System Integrity Protection and is not recommended to keep disabled. If you want to live on the edge though, go for it.
After booting back into OS X/macOS I was able to
sudo rm -rf <Application Path> without any errors.
You can always re-enable SIP after you make your changes.
Note 1: I deleted iTunes once but a system update later put it back on.
Note 2: You cannot easily get deleted applications back because you cannot download them, to my knowledge.
Note 3: If you are just sick of looking at them in Finder, you can hide them by adding a hidden flag to the folder. SIP has to be disabled for this too. I used
sudo chflags hidden /Applications/App\ Store.app/ to hide the App Store from Finder.
Note 4: Certain OS features may depend on apps being present so be wary of what you delete.
You don't. You have no reason to. SIP is stopping you.