I just updated to OS X Sierra (10.12) directly from Yosemite (10.10), so I'm only discovering this issue now. But from poking around the web, it appears this is an issue that was introduced in OS X 10.11 (El Capitan).
Having just installed new system software, I discovered that none of my scripts that rely on the cssend command are working. Since I have cssend installed in /usr/bin for convenience, I figured it probably didn't come over with the new install and I probably just had to install it again.
In trying to do so, I'd follow the instructions in the cssend readme file about going into a Terminal session and executing the command. The system would ask me for my password, but then reject the command with an error stating that "Operation not allowed."
I poked around a bit further and discovered that as of El Capitan, Apple is now restricting certain folders, and without a clunky process (described here: http://stackoverflow.com/a/32590885) to turn off system integrity protection, the user (yes, even the super user, and even the root user) cannot modify the /usr/bin folder.
In reading about this problem, it's been suggested that the proper place for code such as cssend is /usr/local/bin, rather than /usr/bin. The former, /usr/local/bin, is not restricted by the system.
I was able to successfully install cssend in /usr/bin after I followed the instructions in the link above, but this is really getting under the hood in a way that shouldn't be necessary.
I know absolutely zero about ruby, path variables, etc. But since Apple seems serious about keeping us out of /usr/bin from now on, would it be possible for you to rewrite the cssend script so that it lives in /usr/local/bin instead of /usr/bin?