If they used the vehicle specific sensors, no reprogramming is required and all you need to do is drive a little and the system picks up the signals from each wheel. I would question that $48 charge and find out what sensors they installed. I purchased 4 sensors from RockAuto last fall and installed them in my winter rims and no programming was required and they read spot on with my tire gauge. Are you checking all the pressures at the same temp (ie cold)? Temp change can cause a 3-4 psi difference.
How do you know they are off. Did your TPMS light go on?
Your car has the ability to calibrate its own TPMS sensors should they need it. You just have to drive around a while over 30mph.
If TPMS sensors were installed that needed "TPMS programming" they were probably the wrong sensors for your car.
Even so, you can still calibrate them manually yourself. $48 is outrageous. Ask them specifically what they did.