That book was also published to the web in violation of the copyright.
Quoting things from a copyrighted source is fair use. Copying a copyrighted source to the internet for all to read is not fair use.
Not sure if Kerry still held the copyright to his book. A common practice is for the author to transfer his copyright to his publisher as part of a the author-publisher contract.
As for the HRC thesis, my guess would be that Wellesley held the copyright and finally agreed to waive it (perhaps for a fee). A lot of private colleges are in poor financial shape these days.