My understanding is that ZipCar locks/unlocks the doors, probably by interfacing with the car body computer which handles lock/unlock functions.
The engine ignition security system is usually totally separate from the lock/unlock feature despite both functions being accessed from the same piece of hardware (ie the key/keyfob). So my guess is they've interfaced with the lock/unlock system but not the ignition system, which is why the key is still kept in the car for starting.
It's a bit more sophisticated than that--the keys won't start the car without the RFID Zipcard in the vehicle. So they've definitely tapped into the ignition system.
yes, thinking about it even if the ignition system is impossible to adapt to, you can still easily disable it by interrupting the power supply to the immobiliser. It's easy to further disable the ignition but not easy to circumvent the ignition. My guess is that their RFID system probably closes a relay in the power supply for the existing OEM ignition system. That way you couldn't start the car without the correct RFID card, but you still need the key.
http://www.zipcar.com/how/technology