coolbean
Here's a theory. The destruction outside the matrix was not the machine's doing, but our own. Another slant could be is that is was the machines attempting to act in our best interests (see War Games). But what happened after the destruction was that the Matrix was formed by the computers to make a good life for humans until the they could restore the world. The story about their being evil is only part of the control cycle that was their best solution for humans getting out. Could they be benevolent?