A CD is a replicated disc, made from scratch with your content. This will have a silver bottom to it. The manufacturing process to create a CD is commonly referred to as 'Replication'.
A CD-R is a blank disc that we record your content onto. This disc has a greenish / silver hue to it on the bottom. The manufacturing process to record a CD-R is commonly referred to as 'Duplication'.
A CD, like you might buy in a music store by a big name artist, is physically stamped with the digital audio information, kind of like a record, so it can be mass produced easily, quickly, and cost effectively.
A CD-R is burned on a CD-R recorder. The digital audio information (the 'pits') are physically burnt onto a special CD-R disc that contains a special dye that reacts to strong laser light (stronger than the laser that is used to read the disc). It is cost effective for small runs (up to 300).
Regardless of method used to produce the disc, the digital content is exactly the same.