Finally figured this out. I compared my MotionEvents to the two events that get dispatched when I clicked on a button and the only difference was the source. So, I set the source on the two motionEvents and it worked.
....
motionDown.setSource(InputDevice.SOURCE_TOUCHSCREEN);
....
motionUp.setSource(InputDevice.SOURCE_TOUCHSCREEN);
And here's a full version of the method
//=========================================================================
//== Utility Methods ===
//=========================================================================
/**
* Helper method injects a click event at a point on the active screen via the UiAutomation object.
* @param x the x position on the screen to inject the click event
* @param y the y position on the screen to inject the click event
* @param automation a UiAutomation object rtreived through the current Instrumentation
*/
static void injectClickEvent(float x, float y, UiAutomation automation){
//A MotionEvent is a type of InputEvent.
//The event time must be the current uptime.
final long eventTime = SystemClock.uptimeMillis();
//A typical click event triggered by a user click on the touchscreen creates two MotionEvents,
//first one with the action KeyEvent.ACTION_DOWN and the 2nd with the action KeyEvent.ACTION_UP
MotionEvent motionDown = MotionEvent.obtain(eventTime, eventTime, KeyEvent.ACTION_DOWN,
x, y, 0);
//We must set the source of the MotionEvent or the click doesn't work.
motionDown.setSource(InputDevice.SOURCE_TOUCHSCREEN);
automation.injectInputEvent(motionDown, true);
MotionEvent motionUp = MotionEvent.obtain(eventTime, eventTime, KeyEvent.ACTION_UP,
x, y, 0);
motionUp.setSource(InputDevice.SOURCE_TOUCHSCREEN);
automation.injectInputEvent(motionUp, true);
//Recycle our events back to the system pool.
motionUp.recycle();
motionDown.recycle();
}