If pilates is more of a pain in your neck than it is in your abs or butt. Then you are doing it wrong! Let me explain: you should be holding your head in position that challenges your abdominals without causing pain in your neck. If you can not curl up without pain and strain you are not ready for a curl up and you need modifications. This is why it is important to communicate with your pilates instructor about how your body feels. It is also important find an instructor that is trained to give you modifications and customize your workout.
Towel Supported Curl Up
Try doing a curl with a dish towel behind you. Put it down under your shoulders, neck and head. The reach back and grab a hold of the top of the towel and use it support your neck as you curl up. Your neck should remain relaxed and well supported. You should feel your upper abdominals engage.