The way I look at it is like this... would I boo my son if he was playing his heart out, but missed a tackle, or got burned on a pass play? No, I wouldn't. Unless a player is just not trying, I don't believe in booing a player for making mistakes. I hate to see it, but I'm not going to boo them. I'm sure they already feel like crap after screwing up in front of thousands of people.
Directing frustration at poor coaching is a little different, but I'm not conviced that the players know that the fans are booing the play calls.