This doesn't hold for all software patents. Consider something like PageRank. It's in no way transparent from using google how PageRank works, but a patent would disclose that.
Greg also makes a decent point, in that some things that may seem blidingly obvious in retrospect were novel and met a long-felt need at the time. While it may be obvious how it works, the quid pro quo is that you actually invented it and put it in the stream of commerce, as opposed to keeping it as a trade secret.
In the end, under current patent law, as long as the written description discloses the invention and enables someone holding ordinary skill in the art to practice the invention, the patent application won't be rejected because once you use it it's clear how it works.