Because Rex is much, much better at making reads out of the Read Option than Taylor is. That, and he's a much better runner inbetween the tackles.
I don't really buy this. The part about making better reads, that is. Burkhead didn't have to deal with defenses keying on him like Martinez did. After Kansas State, every defense we played last year set out to stop Martinez, at the risk of leaving other parts of our offense undefended. No defense gave Rex Burkhead that much respect.
If you want to run Rex between the tackles, then just hand the ball off. With Martinez on the field, you've got a QB who can run, and the defense has to worry about defending his legs and his arm. Even when he hands the ball off, Martinez can create problems for the defense because they're so worried about him keeping it. You take him off the field, and you remove the most dynamic player from our offense, the guy that keeps defensive coordinators up at night, and you're only doing it so you can run the same plays with Rex Burkhead and one of the other running backs. It doesn't make any sense, it makes the offense less threatening, and easier to defend.
For the record, I think the coaches might agree with me, since at least according to Rex Burkhead they haven't worked on the Rexcat at all this year. Maybe he's just lying, that wouldn't surprise me, but for now I'm going with "the coaches agree with me."
That's the very essence of a Read Option, though. If the defense is keying on the QB, hand the ball off to the RB. How many times last year did we see Taylor make the incorrect read, and get stuffed behind the line?