Copy protection generally relies on certain characterstics of the physcial CD structure that are not and can not be captured in .bin/cue or .iso formats. The .bin/cue and .iso formats are only exact copies of a standard CDs written in a standard format, and they only include information at a higher level of abstraction than the physical layer. For an analogy, consider copying a simple text file from a CD to a floppy. That creates an exact copy of the file, but you can't put the floppy in your CD drive and read it because the physical characteristics weren't copied exactly.
Similarly, CD copy protections tweak the physical characteristics of a CD to push the CD outside of normal CD specifications so that it is difficult to copy but is still readable. You can read a little about one such characteristic here
What I have written here is a very brief overview of a very complex topic, so naturally it glosses over a lot of detail and omits a lot of information. Search around on the web to learn more. As you probably know by now given the source you linked, our friends at club.cdfreaks.com are a good resource for information about copy protection.