That is understandable. I've got an iPad 1 and a nookcolor. Both have glossy and highly reflective screens. My LCD monitors are always the matt finished kind to reduce reflection and glare. So it took a while to get used to the glossy LCD tablets. I love them when it comes to reading in dimly lit situations. But they are not so good in brightly lit rooms, especially with overhead lighting, or outside in daylight. I really prefer to see the text and not my ugly face staring back at me!
One thing I do to help my eyes is to strip the DRM from every book then modify the books to use bold text. I do this even for my eInk reader too. It helps me quite a bit.
Another thing that helped was to just experiement with the screen brightness and page background color until I found a solution that suited me.
On the nookcolor I bought a non-glare screen protector and it works really well, although it took a while to get used to. I tried the same procedure on my iPad but the result wasn't very good. I think it worked well on the nookcolor because the non-glare screen protector is in very close proximity to the text displayed on its screen. However the proximity of the non-glare screen protector to the text displayed on the iPad screen was farther away and so the gritty look of the non-glare screen protector seemed to float above the text and it was way too distracting. So I removed the non-glare screen protector from the iPad.
The nookcolor has a better text reading screen, but I've found that both tablets are very readable when you get all the variables just right.
I have the same problem in reverse with my eInk Sony. It craves a LOT of light and without it I'm going to have eyestrain.