With cross-breeding, I can get characteristic A from some corn, characteristic B from some other corn, and end up with corn with A+B. And also maybe over time taller, or larger.
With GM, I can do a much larger range of things taking genes from fish and putting them in corn (for example), which we currently poorly understand. The kinds of things we would like to do (make plants which grow fast and are hard to kill) seem like exactly the kinds of things that might lead to serious issues (we make a plant which we lose control of, grows fast, and is hard to kill).