The price of the drugs is amortized over everyone with insurance. The drug in question has a total potential audience of around 2000 people in the United States, if I remember correctly, so that means the cost of the treatment will be spread very widely.
Also, the drug he raised the price on was a horrible 50-year-old drug. Shkreli raised the price with the explicit aim of getting funds to research a new drug, with less terrible side-effects.