They aren't actually suppose to be allowed on, but most of the time as long as they behave and are in their carrier, nobody will say anything. As for the buses, thats a different story. They won't let you at all, carrier or not, unless you sneak them on like I do.
And some advice for you since you are coming to Chicago soon, allow more time to get from point A to B if you take the train. They are doing construction -like always- and the trains are DRAGGING BAD!!! Its terrible. For me to get to school it takes an hour!! :-( and I live 5 miles away from my school. Also,
http://transitchicago.com/ is a really good site for information about the trains.