What is the "rootless" feature in El Capitan, really?
First: the name &quot;rootless&quot; is misleading, since there's still a root account, and you can still access it (the official name, &quot;System Integrity Protection&quot;, is more accurate). What it really does is limit the power of the root account, so that even if you become root, you don't have full control over the system. Essentially, the idea is that it's too easy for malware to get root access (e.g. by presenting an auth dialog to the user, which will cause the user to reflexively enter the admin password). SIP adds another layer of protection, which malware can't penetrate even if it gets root. The bad part of this, of course, it that it must also apply to things you're doing intentionally. But the restrictions it places on root aren't that bad; they don't prevent most &quot;normal&quot; system customization.
Here's what it restricts, even from root:

You can't modify anything in /System, /bin, /sbin, or /usr (except /usr/local); or any of the built-in apps and utilities. Only Installer and software update can modify these areas, and even they only do it when installing Apple-signed packages. But since normal OS X-style customizations go in /Library (or ~/Library, or /Applications), and unix-style customizations (e.g. Homebrew) go in /usr/local (or sometimes /etc or /opt), this shouldn't be a big deal. It also prevents block-level writes to the startup disk, so you can't bypass it that way.
The full list of restricted directories (and exceptions like /usr/local and a few others) is in /System/Library/Sandbox/rootless.conf. Of course, this file is itself in a restricted area.
When you upgrade to El Capitan, it moves any &quot;unauthorized&quot; files from restricted areas to /Library/SystemMigration/History/Migration-(some UUID)/QuarantineRoot/.

You can't attach to system processes (e.g. those running from those system locations) for things like debugging (or changing what dynamic libraries they load, or some other things). Again, not too much of a big deal; developers can still debug their own programs.
This does block some significant things like injecting code into the built-in Apple apps (notably the Finder). It also means that dtrace-based tools for system monitoring (e.g. opensnoop) will not be able to monitor &amp; report on many system processes.

You can't load kernel extensions (kexts) unless they're properly signed (i.e. by Apple or an Apple-approved developer). Note that this replaces the old system for enforcing kext signing (and the old ways of bypassing it). But since v10.10.4 Apple has had a way to enable trim support for third-party SSDs, the #1 reason to use unsigned kexts has gone away.

Starting in Sierra (10.12), some launchd configuration settings cannot be changed (for example, some launch daemons cannot be unloaded).

Starting in Mojave (10.14), access to users' personal information (email, contacts, etc) is restricted to apps that the user has approved to access that info. This is generally considered a separate feature (called Personal Information Protection, or TCC), but it's based on SIP and disabling SIP disables it as well. See: &quot;What and how does macOS Mojave implement to restrict applications access to personal data?&quot;

Starting in Catalina (10.15), protection of most system files is strengthened by storing them on a separate read-only volume. This is not strictly part of SIP, and is not disabled by disabling SIP. See: WWDC presentation on &quot;What's New in Apple [Catalina] File Systems&quot; and &quot;What's /System/Volumes/Data?&quot;.

Starting in Big Sur (11.x), the read-only system volume is now a &quot;Sealed System Volume&quot; (a mounted snapshot rather than a regular volume), so making changes to it is even more complicated. See: the Eclectic Light Company article &quot;Big Sur boot volume layout&quot;.


If you don't want these restrictions -- either because you want to modify your system beyond what this allows, or because you're developing &amp; debugging something like kexts that aren't practical under these restrictions, you can turn SIP off. Currently this requires rebooting into recovery mode and running the command csrutil disable (and you can similarly re-enable it with csrutil enable).
Modifying the system volume in Catalina requires disabling SIP, then mounting the volume with write access (and then rebooting and turning SIP back on is recommended). In Big Sur, additional steps are required to disable authentication of the system volume before changes, and afterward create a new snapshot.
You can also selectively disable parts of SIP. For example, csrutil enable --without kext will disable SIP's kernel extension restriction, but leave its other protections in place.
But please stop and think before disabling SIP, even temporarily or partially: do you really need to disable it, or is there a better (SIP-compliant) way to do what you want? Do you really need to modify something in /System/Library or /bin or whatever, or could it go in a better place like /Library or /usr/local/bin etc? SIP may &quot;feel&quot; constraining if you aren't used to it, and there are some legitimate reasons to disable it, but a lot of what it enforces it really just best practice anyway.
To underscore the importance of leaving as much of SIP enabled as much of the time as possible, consider the events of September 23, 2019. Google released an update to Chrome that tried to replace the symbolic link from /var to /private/var. On most systems, SIP blocked this and there were no bad effects. On systems with SIP disabled, it rendered macOS broken and unbootable. The most common reason for disabling SIP was to load unapproved (/improperly signed) kernel extensions (specifically video drivers); if they'd only disabled the kext restriction, they would not have been affected. See the official Google support thread, a superuser Q&amp;A on it, and an Ars Technica article.
References and further info: WWDC presentation on &quot;Security and Your Apps&quot;, a good explanation by Eldad Eilam on quora.com, the Ars Technica review of El Capitan, and an Apple support article on SIP, and a deep dive by Rich Trouton (who also posted an answer to this question).