Kinda have to agree with Davhamm on this one. There is this stigma about dealers that they are out to rip you off. Sometimes, it is well warranted and others, not so much. I had a dealer wanting to charge $110 to reprogram the fobs. I thought that was too much. Another said they'd do it for $50. That's reasonable. Hey, that's the nature of a free market...shop around and go with the lowest cost for the proper work/service/product.
To extrapolate on Dave's post. How many programmers took how many hours to make that software? It isn't Microsoft Word and the software itself is going to have a VERY limited market. I'd bet HPTuners ($400-$600) or Adobe Photoshop ($800-$1200) have a bigger market. Then there is the hardware the software runs on, the cable to connect to your car, the tech's time to do the programming (which can take more than just a couple minutes), his health benefits, his clothing or other related work costs for that tech, his training on the software and procedure, the electricity to power the hardware and the lights in the building the programming is done in, the rent or cost of the facilities the work is performed in, taxes on that income, water to the facility, heating costs of the facility, the salary of the person at the payment desk, the cost for the hardware and software to process the work order, the salary of the service tech who took your car in, the cost of the paper and ink to print the work order and/or sales receipt, the cost of the complimentary coffee and donuts in the waiting room...
...oh, and since no one has a business that they expect to operate for free, the factored in profit margin for the dealership.
Just something to think about when you look at what goes into the pricing of a service at a dealership...or even a regular mechanic's shop.