Why use difference amplifiers over instrumentation amplifiers?
But is the only reason one would use a difference amplifier over an
  instrumentation amplifier cost?


No, one great advantage that a difference amplifier provides is substantial "beyond the rails" operation. Consider the ADI difference amplifier below: -



Look at +IN - it sets the scene for the voltages at the actual inputs to the internal op-amp. If "REF" is tied to internal ground then +IN can approach nearly double the voltage that is applied to +VS.

This cannot be achieved with an InAmp. 

But, other difference amplifiers can provide even bigger limits on the terminals such as this one: -



This can operate with an external input that is about ten times greater than the supplies to the chip.