It seems the most important issue is the chicken-and-egg problem: Chicago doesn't have a large magnate company with lots of b/millionaire founders that then fund the ecosystem. Groupon was once thought to be just that company but hasn't turned out good.
The other problem seems to be plain and simple: being in the middle of nowhere doesn't help. From the article:
"The University of Illinois at Urbana-Champaign turns out more engineering graduates than any U.S. school except the Georgia Institute of Technology, yet no tech scene has grown around it — or 140 miles north in Chicago. Fewer than half of these engineers remain in the state while 10 to 15 percent have gone to California in each of the past five years"
For a young person, there are many more opportunities to do sports (mountain biking, hiking, skiing, kayaking) in other places.
As a final point: Chicago, long the city of broad shoulders, is not famous for its counterculture, like Seattle or Portland is, so loses that chance for attracting people, too.