Don't cross the beams, don't aim at glass... same thing, really. You don't want your coffee table to melt, so you best move it.
If the Infrared the Wii Remote uses to communicate with the Wii does come in contact with the glass, it could definitely screw with the controls. I believe what glass does, is disrupt or distort the Infrared, or partially reflecting it away from where you're aiming the Wii remote. So yes, it might be a good idea to move the coffee table or sit at a longer distance from it.
If your sensor bar isn't at the top of the TV, it might help to change that. If you do this, make sure to go to the Wii's options, and find the "Sensor Bar" tab to change it to calibrate for being on top of the TV.