When I'm reading anything on an iPad, I triple click the home button for the accessibility setting. I don't know whether I'm undiagnosed dyslexic, but I can't honestly seem to read it otherwise. I find it really hard to read black text on a white background. Particularly on an LED backlit screen. I do it on the MBP too, on a side note; I never had this issue with matte screens.
If you're suffering actual pain in the eyeballs, it's probably a brightness thing. Either it's too bright or you're reading in a dark room and they're becoming strained. I found I was having the same issue on my old 27 iMac, full brightness + dark room = hello floaters.