He was still bounded by some limits in the Matrix though. He could never teleport. His limitations seemed to be re-writing electronics within the Matrix, which could be explained by his skill as a hacker amplified.
Part of the premise is that there's still a set of rules, and he can break some of them but not all of them. He doesn't have the power to teleport as seen anywhere in the movies, but he can fly, really fast. In the 2nd movie, he's 500 miles from Trinity/Morpheus/the Keymaker, and he has to fly there - which he can do really quickly - but he can't be there instantaneously. He can't even duplicate himself like Smith does. He's still only one mind, in one body.
And that's an important theme, btw - that he's both God-like, and man-like. An obvious parallel. In the very first movie, he "moves faster than I've ever seen anyone move before" according to Trinity when he goes into bullet time. He ruefully glances at a graze wound and says "Not fast enough." He can stop, by the end of that movie, the motion of bullets. But there's no indication that if he let the bullets continue on their path, that they wouldn't kill him, or that he could turn them into dust when they contact him, etc.