Derszoger: You’lle notice that Bar Ilan doesn’t use pdf copies of the pages of printed editions of the seforim, they merely reenter the text of the sefer into the program; its essentially the equivalent of you sitting down and typing the entire Igros Moshe into MS Word to have your own copy of the sefer. Bar Ilan is using the though-product, the Torah itself. They aren’t reproducing the efforts of publishers who invest money and time into producing the sefer.
Better question is how does Otzar HaChochma do it; they use pdf copies of the actual pages of the seforim, and unlike Hebrewbooks, they make money off the effort. Could be they only use seforim whose copyrights have expired, and for others they pay the publisher for use. But I don’t know.