You'd be surprised how much the loaded folks can pay for a guitar that are worth less than their market value. Plus, I imagine they only earn a portion of their income from actual sales of the guitars. They provide luthier service as well.
And trust me, I have tried negotiating. While its possible to lower the price down abit, I have never seen a similar instrument sold on soft for a higher price than those sold in used guitar stores. If you have cash to spare, and really dig a certain instrument they have on sale there then I say go for it. However, if you want a 'value-for-money' deal, I say look elsewhere.