1) It's lighter and smaller and thus easier on your hands to hold it. My hands begin to hurt after holding the iPad for more than two hours. Reading is something I can do for hours without interruption.
2) I thought that an advantage of the ipad would be that I can read with the lights already out. I was wrong - staring at the illuminated screen quickly hurts my eyes in an otherwise dark room. Interesting: Watching videos is no problem, but reading apparently is something I use my eyes differently than watching a movie.
3) The distraction factor is huge if reading your mail, hacker news or google reader is just a small home button press away. I can't. get. any. serious. reading. done.
For me, reading a book is an activity I'm doing for hours at a time if I finally find time. Then, being distracted, having to carry a heavy device or hurting my eyes all are not optimal solutions.
Hence, if I'm reading, Kindle is my device.