Supply and Demand.

Small breeds are often in high demand and since they have small litters (supply), the cost of them is higher.  In the case of cross breeds (designer breeds) the high demand for them increases the price regardless of the litter size.

High maintenance.

Since small breeds are more fragile they require more time and care on the part of the breeder which increases their price.  In the case of English Bulldogs (not a small breed) they require a Cesarean in order to give birth and they also need to be hand fed since the mothers often times can roll over and crush their young.  Because of this, English Bulldogs can cost up to $2800!