It's never a good idea to go at it with a ref. Exchanging words or being frustrated is one thing, but when it escalates beyond that, nothing good will happen. And as Rajon Rondo found out on Sunday, throwing a ball at a ref just doesn't end well.
Rondo was upset about a non-call underneath the hoop, and his frustration boiled over during a dead ball. It all began when he drove to the hoop and took quite a bit of contact, going to the ground and immediately looking for the call. It never came, but Rondo was ejected moments later after tossing the ball to/at the ref.
Just a bad situation all around. The ref wasn't really paying attention to Rondo and there was no way he was catching the ball anyway. When Rondo decided to give him back the ball, or toss it at his chest, the ref had his hands up to make a call. One could argue he was just tossing the ball back to restart play, but it simply doesn't look good.
It's probably a safe bet to assume the league will take a look at this.