That is hardly representative of both Chicago and San Francisco's startup scene. I am not sure which is more shocking to me, the fact that you are posting this on the Atlantic (an extremely well respected publication) or the fact that an editor approved this.
A. The San Francisco map doesn't even include Menlo Park, Mountain View, etc. The San Francisco startup scene is even larger than you depict. B. You don't list the San Francisco startups as you with the Chicago map. C. You just Googled the locations of a few well known Chicago startups and just plopped them on the map. Simply taking a few minutes to search you might have found 1871, a startup incubator located in Chicago's Merchandise Mart that is the home to several HUNDRED startups. http://www.1871.com/about/ D. The scale on the maps are not comparable. E. This is simply unintelligent and a perfect example of the poor journalism we see today.
In Short: Thank you for wasting five minutes of my life with your last minute-deadline submission that contributes zero value to society.
http://articles.chicagotribune.com/2011-09-08/business/ct-bi...
http://kiddermathews.com/downloads/research/office-market-re...
Or as others have pointed out, people will click on links with their current city mentioned. I am sure it would have evoked the same reaction from people in LA if they overlaid Santa Monica/Venice Beach over SOMA.