Kat, the rubber "u-tube" is the vent for the window motor. With it removed, water will be free to enter the motor and ruin it!
I posted some photos in the window regulator thread of what my motor looked like on the inside with this tube missing! You definitely want to put it back on!!!
Edit: found my photos:
http://www.vehicross.info/forums/sho...2&postcount=23
And another post blow it.
http://www.vehicross.info/forums/sho...5&postcount=26