I took me two years to do a roll-up after recovering from a serious injury!
I teach the roll down phase first when clients are very weak. The eccentric contraction builds up their strength, lessens frustration, unnecessary gripping and the potential for injury.
I tell them to bear the discomfort (not the same as pain!) in the front of the neck (which improves as they get stronger) but to stop if they feel they need it. I also ask clients to rest if/when they feel the work in the back of the neck, usually a compensatory strategy with muscles not relevant to the action coming in to help very weak anterior neck muscles. I find that these front of throat muscles are really important to provide support for our head (especially those with forward head posture) and my clients have much better health now in that part of their body too because of their Pilates practice.
Here is a link for a beautifully explained anatomical explanation of sit-ups and Ab Curls: http://bit.ly/I1S7nk. This applies to Roll Ups too, except for the difference between legs bent or straightened, putting less stress on hip flexors because of the relationship shifts between points of origins and insertion.