The value created by the work that you did for hire does not have to translate in to your salary at all, just like you're not going to have to share in the losses if the project turns out to be a dud. When a welder helps to put together an oil rig that then either makes millions of dollars or explodes, sinks and causes billions in damage the fact that he did it as a salaried employee shields him from the damage just…
Wealth is all about percentages and the standard profit percentage share for professionals and engineers, "big-corp" or otherwise, is 0%. These programmers left to start their own trading companies, likely because the salary bumps being offered (a measly $45,000 extra on $150,000 base salary, in the example) were insulting compared to the revenue being generated directly from their work. That's demonstrable value. Consider: a 1% profit share from the example in the article would be over $300,000 per year. Not a large bonus at all for a financial managers or executive, but not an outlandish bonus for a highly valuable member of a lucrative enterprise, either.
Your last paragraph sounds a lot like, "keep your head down and be thankful you have a job." I assume you're just defending the status-quo and pointing out the tradeoff between sharing the risk/reward and being comfortably salaried. You can't possibly be implying that programmers or other skilled professionals shouldn't even try to negotiate better contracts, right?