Yes, make it executable with that chmod or 'chmod +x' as well.
Alternatively you can download it to your pc and copy it to the root directory and then move it across at your leisure. Eg if you're on a linux pc:
On your PC:
wget http://ck.kolivas.org/apps/cgminer/antminer/s3/4.6.0-140908/cgminer
scp cgminer root@192.168.1.99: [Or whatever IP address your S3 is]
ssh -l root 192.168.1.99
If you're not on linux you can use winscp for the scp part and putty for the ssh part
On the S3 after login:
/etc/init.d/cgminer stop
mvusr/bin/cgminerusr/bin/cgminer.bak
mv cgminerusr/bin
/etc/init.d/cgminer start
Even after rebooting the S3 it will continue to use the new binary unless you issue a complete hardware reset.