If sit-ups make your neck hurt, maybe try some different exercises. There are lots of ab exercises that would accomplish the same thing as sit-ups. My favorites are crunches, leg raises (I do them with 5 second holds at the bottom and top of the motion), flutter and/or scissor kicks, and bicycles. All of these are a lot easier on my neck than sit-ups.
Check out
http://www.self.com/fitness/workouts...category%3Aabs for lots of ab exercises that don't involve any special equipment. This same site suggests that when you do sit-ups, press your tongue to the roof of your mouth, just behind your teeth. This is supposed to help you align your head properly.