Well that pretty much is the game rationale for it: Your programs really are your Matrix attributes. The Matrix has a lot of analogues with the Astral, and this is one of them. In astral projection, you no longer use your physical attributes. In virtual reality, you no longer use your mental attributes. In both cases, the rules of the alternate reality require different "attributes." On the Astral, you use mental attributes instead. In the Matrix, you use software.
Oh, and don't forget that you can even replace your attributes in the real world, with 'ware like cyberlimbs. I don't see attributes as fundamental, but more like very broad skill groups. Not many things can cover the same scope, but in limited situations (like tracing a signal or lifting something heavy) you can cover them just fine.