If you want a cheaper hotel that's not in a questionable area, then I think the O'Hare suggestion is a good one. If it's a weekday morning interview, I would advise NOT taking a shuttle/taxi, as the traffic going into downtown will be crawling along 90/94. The Blue line will be faster, but it will indeed take an hour or so. Also, there are actually two Blue line routes, which split after downtown. Both will take you to the right area (IMD, where they split), but I believe the 54/Cermak Blue line will take you much closer to UIC or Rush (at the Polk stop). Check it out here:
http://www.yourcta.com/maps/systemmaps.html
Same idea for Midway airport--cheaper but nice hotels are closer to the airport. The Orange line goes directly from the airport to downtown, where you'll have to make a transfer to the Blue line. Again, about an hour or so. I'm not sure how I-55 North is in the morning rush hour, but I believe it's not as bad as 90/94. So in this case taking a shuttle/taxi may be faster.
If it were me, I would actually stay at the youth hostel downtown. It looks quite nice from the outside. It's cheap ($35) and you just need to walk a few blocks to catch the Blue line in downtown. The ride will only be a couple stops--probably 15 minutes travel time. But if you're a light sleeper this may not be ideal. Check it out here:
www.hichicago.org/
Good luck!