Are there many coffee shops in Chicago that aren't big chains like Starbucks?

Tons! While you're certainly going to find more than a couple Starbucks and Caribou Coffee's around (although Caribou is closing most of theirs or converting them into Peet's Coffee) you'll also find some really cool, quaint coffee shops. I've felt very welcome in some, and sorta like an outsider in others. I think it really depends on how you approach them. Red June is really good, as is Ipsento, which are both in Bucktown, but there are a few in the Loop and pretty much every neighborhood as well. It's not Seattle, but Chicagoans love their coffee!