If you installed cgminer using the referenced guide, and you are trying to mine scrypt, it wont work.
cgminer does not enable scrypt mining by default, when you ./configure it, you have to add the argument of --enable-scrypt. By default, cgminer only enables gpu mining in linux, so if you are mining scrypt or asics, you have to enable those options when compiling, which is why its telling you that it doesnt recognize --scrypt as being valid.
So, redo install cgminer and use these options (also, that guide enables cpumining, which cgminer doesnt even support anymore).
$ sudo su
# cd /opt/
# git clone git://github.com/ckolivas/cgminer.git
# cd cgminer/
# ./autogen.sh
# CFLAGS="-O2 -Wall -march=native" ./configure --enable-scrypt --enable-bflsc --enable-icarus --enable-avalon
# make -j8
This will enable scrypt mining, as well as support for BFL ASICS, Avalon devices, and block erupters in case you want to add them later.