A question I can answer! Bought my 1st laptop/macbook pro 13" recently and I'm having the same problem, which I predicted...
I noticed that a lot of my college friends that use their macbook pros as their primary and only computer complain about headaches and eye strain. I've been using mine for only a couple months now and have been experiencing massive headaches.
I've always experienced eye strain with computers. I've been using desktop PCs my entire life and experienced eye strain anytime I stared at the screen longer than 30 minutes. Although a bit more intense, this eye strain was similar to the strain I experience when I read or when I watch TV for a long time. Just "tired eyes."
As for my recent eye strain from my MBP 13", I feel like the LED backlighting is slowly ruining the health of my eyes, more than any other screen/TV/phone. There's no pain or strain, just this dull sensation towards the back of my eyes and frequent headaches. My conclusion is: CCFL and LED = different lights = different eye strain/pain. This day and age it's unavoidable, any lights from cell phones, computers, TVs... that are directed/projected at you are going to cause harm to your eyes. When I get the money, I plan to buy and use a projection screen.
As for the headaches, I guess I'm just more sensitive than others to lights, radiation, etc.
Most helpful methods for me:
-Keeping my distance from the monitor (difficult on a 13").
-20-20-20 rule: every 20 minutes, stare at something about 20 feet away for 20 seconds. I've taken this to another level by taking a walk every 40 minutes.
-Position your monitor/computer so that you are looking slightly DOWN at the screen. Your eyes looking UP at things cause more strain.
-If possible, close your eyes for a few minutes with your head back but don't fall asleep at our job.
-Email Steve Jobs and ask him to make alternative non-LED screens. Some of us don't care or need the bright, colorful, top-quality picture that LED supposedly provides.
-Avoid using your computer, if possible. Print out and read long material on paper.