It can't shoot down the aircraft, but not shooting it down means other people are harmed.
This is why the ends don't justify the means. As soon as someone says "the ends justify the means" it gives everyone an excuse to use any solution to a problem, even if it isn't the best solution. An intelligent robot would figure out some way to stop the plane without killing anyone.
...and how do we even know anyone is going to die? Can the robot predict the future as well? For all it knows, it merely appears that people are going to die, but if it does nothing, the passengers on the plane will regain control and no one will die.
...or maybe the robot simply had bad information and there's actually nothing wrong at all.
Also, while it doesn't apply in this case since the people on the airplane will die whether the robot does anything or not, consider a situation where a robot (with magical all-knowing predictive powers) can save ten people by killing one innocent person. What makes the robot so special (aside from the magical all-knowing predictive powers) that it gets to decide who lives and who dies? Even if we assume that ten lives are better than one, how do we know that one person wouldn't go on to save thousands of lives? Sometimes the only moral choice is to let fate do what fate is going to do. Just because you'll never know what that one innocent person might have done later in his life doesn't mean it's OK that you killed him to save ten others.
The simple fact is that the ends don't justify the means. The morality of one's inactions is an important thing to think about, but nowhere near as important as the morality of one's actions. If the world were full of people who often fail to do good things, but who at least never intentionally do bad things, it'd be a fairly nice place, especially compared with a world where people often do bad things because they think they're good, a.k.a. the world we have now. Even those terrorists on that plane think they're doing the right thing, and so a set of morals that allow you to kill innocent people as long as you have a good reason aren't all that useful.