The author does not understand that salts primarily protect against rainbow tables (pre-computation attacks). He assumes the purpose is to increase brute force search complexity or somehow add additional secrecy, and is correct that it fails at both.
If you are already using user specific salts and a strong SHA hash, the next place you should be looking to add security is increasing the number of rounds (i.e. sha(sha(sha(hash+pass)))) or switching to bcrypt (which takes advantage of an expensive key setup phase in blowfish to make brute force searches very painful).