In The ethics of handling -- and manhandling -- a book, Patrick Reardon examines the relative morality of dog earing pages, underlining, and even more drastic crimes against the printed page.
An undergraduate professor of mine demonstrated the value of adding my own layer of information, atop the author's, by making systematic notes, symbols, and markings. Today, as a book collector, I won't write in volumes that I've purchased for the collection, but if the book is mine to consume, then I typically do "violate" it with the mark-up gleaned from my dear old prof.
I don't concern myself with how my markings might interfere with the next reader. I got over this with a somewhat painful emotional experience many years ago. I had lent a monograph to a professor, in graduate school, and when he returned the book I asked him how I liked it. He said its conclusions were exceeded in their obviousness only by the notes that someone had made in the margins. Ouch. I became self-concious about my markings for a while thereafter, but have since gotten over it.