Prices are set by the value that the buyer places on the good/service. The problem with the WoW Auction House is that we have no idea what things are selling for. We know what they're being posted for, but that's not a very good proxy.

That said, there are a bunch of reasons why you might sell a crafted good for less than the materials: one of them is that you used the materials to skill up, and having 40g for all of your gems now is worth more to you than spreading out those sales and getting 10g more per gem over time. There's a time-value of gold in WoW directly analogous to the time-value of money in the real world: having 10g now is always better than having 10g 3 months from now.

All that to say that just because YOU think that taking your time and selling the gems for a larger markup, but more slowly, is better, doesn't mean that the other buyer shares your opinion on the value of the gold. If, for example, you've got 15,000g in the bank, and everything you've ever wanted to buy is bought, you have no need to have the gold rightnow. If the other person is still saving for their flying mount and is getting really sick of running along the ground, having all of that gold ASAP is worth more to them.