The major difference between the code reader and VAG-COM is that the code reader is limited to reading codes only on certain modules while VAG-COM is the equivalent of the VW factory tool allowing full access to all modules. With VAG-COM, you can code modules, perform bi-directional tests, query measuring value blocks, log and display data from those blocks, perform adaptations and basic settings and more.
If all you need to do is read codes, then the code reader may be the tool for you. If you want to be able to maintain your car yourself, you may find the code reader inadequate to do so.