Most people feel some neck tension when they lift their head off the ground when lying down. To ease tension in your neck, you must begin any movement by first engaging your Powerhouse (your core).
When your abdominals are engaged you will be flexing and lifting your head using your whole spine rather than just your neck. This will take some of the tension out of your neck and put it in your abs.
Avoid looking directly at the ceiling when lifting your head off the ground. Instead, practice looking toward your navel or around the middle of your thighs.
Finally, it is also possible that the muscles of the Powerhouse are fatigued so your neck is taking over the work. If this happens you should stop, and take a break. Sometimes it only takes a moment to recover before you join back in the exercise.
Never suffer or push through neck or low back tension at any time. Pilates is about precision, control and efficiency, so take breaks when you need them.
Listen to your body and know that with practice and patience you will develop the skills necessary to avoid neck tension.