So I went ahead and made a bag. It is canvas, about 2.5' by 3.5', and has a zipper at the top. If I strap the wheels to the side of the frame, remove the seat and pedals, and put the bars in my messenger bag, I can slip the bike inside with room to spare. Materials cost $30. I have a peice of seatbelt that ties to the frame on either end, so the bag is not supporting the bike, only concealing it.
I tested this thing out for the first time on a bus from Chicago to Madison, WI. I rode to the station with the bike bag in my messenger bag, dissasembled and packed the bike in about 5 minutes, and waited for the bus. Their policy is that you pay $10 extra to bike an assembled bike, and only $5 if it is in a box. They treated my bag like a regular peice of luggage and I payed nothing. It took another 5 min. to assemble the thing on the other end. I had the same experience on the way home, the bike road for free. Nothing was damaged, dinged, or scratched. My next test is to actually take it on the Metra. They have a reputation for being hardasses, so this will really prove the bag's worth. I'll post some pics of the trip.