Why do I get “Operation Not Permitted” when I try (as root) to delete a file that does not have the `restricted` flag set

I know about SIP, so when I could not delete a file as root from a Mac running El Capitan, I checked for a restricted flag using ls -lOd and saw that the file had no flags. So why is it that I still cannot delete it? The ls command also ruled out the uchg and schg flags and I’m doing this as root so I don’t need to worry about chown.