Combination of factors. Frustrating on-court behavior including time-wasting, over-the-top fistpumps and well-timed MTOs. Esthetically unpleasant playing style. Personality not that appealing to some.
In addition, Nadal's MTF fans have a unique ability to make people dislike their fave.
I disliked Nadal before I found this board, but his fans certainly haven't done him any favors.
What I really dislike about him, more than finding his face and game unappealing, is the fact that everyone talks about how humble and gracious he is, and he wins a sportsmanship award, despite all his unsportsmanlike actions on court. He wastes about as much time as Djokovic, stalling opponents whenever possible, but no one has every called Djokovic a good sport. What's more he'll celebrate like crazy even defeating a 30, 40, 80 ranked player, especially if he was down a break or a set. His recent sore loserness against Djokovic has been especially grating.