I think when most fans boo a player on their team, they're not necessarily wishing ill on that player, they're complaining that said player is still on the team or is being used in that situation.
In Chicago I once saw Ozzie Guillen get booed as he walked to the mound to take a popular relief pitcher out of the game (Bobby Jenks, back when he was a newly-called-up prospect being eased into the bullpen). Gotta be an ego boost for a young man to hear a crowd boo the manager for taking you out.