3 reasons:
1) Commodity prices for chocolate are going up, due to poor farm management, soil degradation, political unrest and war where its grown, and global climate change. See here for some of the problems. Other ingredients' prices (like almonds) or specialty or premium ingredients (like organic certified whatever) also up the wholesale cost.
2) Really good truffles are handmade, which is always more expensive than mass produced just in labor costs alone. Those little swirls that identify the filling don't just magically appear.
3) People are willing to pay the prices set by the chocolatiers, so prices stay as high as the market will allow. That, and if all you make is chocolate, the per-piece has to be high enough to cover material, labor, rent, insurance, etc. etc. to keep the business afloat.
I do like chocolate, but high prices are good for my diet since I can only have a small amount of the good stuff as it's all that I can afford.