Okay, but if you look closer I bet you can see the problem there. That chart refers to the "Median US Household" defined thus: annual income of $54,286 (mean third quintile U.S. income); owns a home valued at $178,600 (median U.S. home value). In Silicon Valley, that comparison would be between someone earning poverty-level wages who inherited a shack on the edge of town versus a reasonably comfortable midwesterner.
In this comparison between IL and CA we're making, the cost of living and real estate completely dwarfs the tax burden in its effect on the lower ranks in Northern CA. The difference in income tax would be hugely in favor of IL if you were at the very high end. Perhaps there's some middle ground where IL looks worse in the comparison, but I wonder if you'd really be better off financially in California. (edit: Northern California)