The difference you're talking about is often referred to as "fixed width" versus "liquid" or "fluid" layout.
Fixed width layouts are MUCH easier to design than liquid ones. When you design a liquid layout, you need to control many more aspects of the display. What happens when windows shrink beyond a minimum width? What parts of the window can stretch, and what should be fixed-width columns? Is there a maximum for "body" after which layout will look bad? (I've seen liquid layouts that were almost unreadable on a 1920x1080 display.)
A second reason, vying for the position of most-important, is that fixed width layouts are predictable. In a largish company with a "creative director" or "graphics designer" who is different from the person implementing a web site, the wireframe or example site will likely be done in Photoshop, approved by a manager, and handed off to a web programmer to implement in a CMS (for example). The web programmer doesn't care about fixed width vs liquid, he just wants to get the site implemented the way it was approved by his manager. And variations will require additional approvals, and it becomes impossible to improve a layout that will be different for each browser.
And a third less-important factor... There are a number of web site analytics tools that measure a "heat map", and heat maps are virtually impossible to implement in liquid layouts, since links do not appear in predictable locations on the page.