I had the same problem and then I worked it out. You have a number of options.
1. Put the camera in M mode, but then you have to select the shutter speed throught eh viewfinder and the aperture of the lens (but you can set the aperture you want and then press the green button, the camera will stop down to the aperture you have set, meter the light and suggest a shutter speed).
2. Back to green mode, it depends what autofocus setting you have on the side switch i.e. AF.S, AF.C or MF. In AF.S mode, the camera will not take a picture until it is perfectly in focus i.e. the little green hexagon has appeared in the viewfinder and the camera has bleeped, if you have the bleep switched on. In the other two modes it will take the picture whatever.
It took me a while to fathom, but its quite simple really. Hope this helps.