It would be unfair to say that Matt Damon hates the character of Jason Bourne; he's done very well out of the 'Bourne' series of movies, and wouldn't have come back to the character so often if he hated it. It's just that he happens to despise one of the films, and he knows exactly who to blame for it. That's Tony Gilroy, and the script he provided for the third film, 'The Bourne Ultimatum.'
Damon had less-than-flattering things to say about Gilroy after the film was made, including a suggestion that Gilroy took a huge payoff from the production company and then just phoned in the script. Damon worked as hard as he could to improve what he was given - so if we're to believe Damon, what ended up on the screen was better than what was on the page - but apparently, the original Gilroy script was 'unreadable' to the point it would end Gilroy's career if Damon posted it online.