The 2011 Zero uses the Main Bike Board (MBB) to filter the throttle signal before it enters the Alltrax controller.
If you read through some of the threads in the '2012 and earlier Zero' section of this forum you will find posts by Electric Cowboy and Doctorbass where they talk about changing the throttle mapping via programming the MBB. In that software you can change the control from speed to torque or both and the upper/lower limits and ramp rates, etc.
If you don't have a Zero MBB then you could use a Throttle Tamer or Picoamps throttle filter module to convert your throttle signal so that it acts more like a current/power/torque control rather than a voltage/speed control.
http://greyborgusa.com/product/throttle-tamer/description of operation here
http://endless-sphere.com/forums/viewtopic.php?f=31&t=51460 I have purchased one of these to install on the ZEV 7100 LR as the throttle on that is speed control and acts like WOT until it gets to the speed you set with the throttle and so is very jerky and not very nice when compared to my Zero electric bike or my Yamaha MT-07 ICE bike.
You could try building your own throttle tamer if you can solder a circuit or program an Arduino.
http://endless-sphere.com/forums/viewtopic.php?f=2&t=78&start=200