The person making 1.2 million isn't just a programmer, but he/she also understands the business well. More so, he/she is an integral part of the business.
EDIT: I have now read to the last page of the article, and I guessed right!
What's the intellectual kit needed to become a programmer at a high frequency trading firm?
http://www.nvidia.com/object/computational_finance.html
http://io9.com/5784758/the-speed-of-light-could-turn-the-mid...