Sometimes these are the same person, but in those cases that person almost always has a profit sharing contract, not only a base salary. (And if they don't, they're crazy.) The fact that the programmers in the article only had base salaries leads me to believe that they weren't the actual creators of the trading algorithms, so they don't really deserve a slice of the profits anyway, because someone else a) created the profit machine and b) is taking all the risks of running it.
What really happens is that these programmer guys learn the trading secrets after a few years on the job, then depart to a different firm to recreate the machine themselves. There's no oppression or revolts here.