I would say it's just supply and demand at work.
While the lower level gems drop regularly in game, especially if people are farming for gear, the higher level gems either don't drop, or drop rarely. Personally, I'm just starting Inferno and I have a bunch of gems just lying around (around a dozen of all the square gems and a half dozen or more of each of the flawless square). I also have an entire stash tab devoted to gem storage for all the gems I've picked up along the way. If every player has this sort of stash, you can see that there is a large supply at work. Conversely, there is very small demand for any particular tier of gems. Think about how many you actually use compared to how many you pick up regardless of quality.
From this, you can see that the jewelcrafter much like the blacksmith is really intended for higher level characters. These people:
- Have a large disposable income. I'm just starting inferno (reads: getting my face smashed pre-Leoric), and I can still make ~100k within a relatively short amount of time,just vendoring items. The Auction House can inflate this further very quickly.
- Want and need the higher level gems which don't drop.
This leaves these people with two options: get their own jewel crafter leveled, or buy gems at vastly higher prices on the Auction House. Keep in mind that the last three tiers of gems are only available via recipes which drop. These recipes are individual gems also, so there are a total of 12.
For everyone else, there's the Auction House which has large numbers of gems of lower quality that other people no longer need. These are usually gems that have dropped, not ones that have been combined using the jewel crafter, which explains the lower cost.