Whats the difference between these two? They seem to both do the same thing not to mention both applied to the bitmap through applyFilter().
The color matrix filter is, as the name and usage implies, an image filter effect available in Flash (documentation available here).
Pixel Bender is the generalised language and tools provided to allow you to create your own custom image filters. More pixel bender info here: http://www.adobe.com/devnet/pixelbender/
So, at the simplest level, the colour matrix is a built-in filter and pixel bender allows you to create your own filters.