Simply: Because it punishes users who don't conform to your expectations of a desktop computer with a modern wide screen. Basically, the more assumptions you make about minimal screen width, the closer you get to earning the dreaded "Works on my machine" distinction.
One major advantage of a wide screen is that it is possible to have multiple windows, tiled. If the (web?) designer makes the assumption that the user will always maximize the window, he/she stands in the way of some very efficient workflows. Basically, just because the user bought a large screen, they didn't give you the permission to occupy all of it with your application.
There is a multitude of devices and platforms (and has always been). Just because desktop computers tend to get larger screens lately, this doesn't mean that all devices which run your application have them. This is especially true of web applications, which have to run on all kinds of platforms, but it can happen that users want to run your Windows desktop application on a netbook sized computer, a small screen embedded somewhere in an industrial setting, and so on.
Users are not obliged to buy the latest and greatest hardware. Many non-IT-affine people out there still use ten year old monitors in a 3:4 form factor and low resolution. And they have an expectation that your application runs at their computer too.
And don't forget that most websites out there are still about text. Longer lines are very detrimental to readability. The optimal reading configuration contains 60-70 character wide lines which follow vertically in a linear manner. And while the user is engulfed in reading, he doesn't want to have anything beside the text. But if you put something else there, he will ignore it anyway. This is a special case (applications can sometimes make a good use of a right column, see Remember the Milk and Mendeley for decent examples), but it is a very common case.
Besides that there is no need to restrict users when you can avoid the restriction, I also find the "wasted space" mentality very disturbing in a designer. Just because you could overload your user with information, it doesn't mean you should. Focus on providing the user with the exact set of information needed for the current task and don't distract her with extra columns she probably doesn't care for.
There are very few cases where extending a single application on the whole monitor width is beneficial to the user. The one is data which is naturally present in a huge grid. This is normally designed by still using the grid, and downgrading to a listlike view when a smaller window size is detected (not display size! remember tiling). The second case is when the user has a viewport on a coherent visual object, for example in a 3d modelling tool, photography postproduction software, or a 3D open-world game. This is usually no problem, as the tools are floated somewhere around the edges, and the viewport is automatically sized to the available window space without the need to reconfigure its content.