I have a cylinder that I want to put an opening for a door in, I made a rectangle and placed it going through where I want the hole, but when I do try to subtract it it doesn't do anything, while it will do it for another rectangle. Is there a way to do this?

you'll have to patch around where the door goes.. no way to subtract anything from a patch and also... last i heard csg subtract was evil

CSG subtract isn't evil unless you use it against a huge conglomeration of small brushes or things like...patches.

You have only a few options here, and none of them is quite satisfactory. First things first, try using Plugins > Bobztools > Split patch--this will turn your cylinder into 4 bevels. Now, you can either move the bevels a few units apart and put in normal brushes in the spaces, and then cut the brushes to make your doorway; or, you can select one of the bevels, add a few rows/columns to it, and move the verts around to make a doorway.

CSG substract is still evil.