Right-click on the brush, and click on "Tie to entity..."
You should be on the tab "Class Info". Make the class "func_seethrough" using the dropdown box.
In the attributes list, select "alpha for players" and set it to how thick you want it rendered. If you want it to look like it's not even there, set it to zero (and do the same with "alpha for commander"). If you want it to look like a window, but you can still see through it, apply your window texture to the brush and then set the alpha stuff to somewhere in between 0-255. Experiment with the numbers to see what you like.
If you want to, you can always set the commander and player alpha variables differently, so the commander might be able to see through it, but the players see just a wall.
*EDIT* aww, Recoup beat me to it.