So end of X-Men 2, Professor X is connected to all the mutants through Cerebro, giving them an incapacitating headache. Then it gets switched, and he’s doing it to the humans instead.
So, first, he’s crashed every airplane flying. Both episodes are for 5-10 minutes. People can’t do anything. First he got any mutant pilots, then humans.
Second, he’s caused millions of car crashes. Also, surgeons, construction workers falling, etc.
So wouldn’t he have been hunted down by the world? Maybe it wasn’t his fault, but no way people stand by with one man having the power to kill everyone. He’s killed maybe what, a million people through both episodes?
Does anyone, outside of the X-Men, know he was responsible for that? Well, Magneto, sure, but I don’t see him going to the government with that information. My guess is that they gave the President enough information to pin the blame on Stryker, but not enough information for them to work out how he did it, or Professor X’s role in it.
As a possible “out,” they never did say how many minds he actually grabbed. Sure, given enough time he could have expanded his control over the world and wiped the map. However, they didn’t say how far he got. Possibly he only managed to attack the few people close to the bad-end of Saskatchewan, or whereever they were.
The assumption that every airplane in flight crashed as a result seems unreasonable to me. As I understand it, commercial airliners run almost entirely on autopilot while cruising. If everyone on board a plane is incapacitated for 10 minutes, the plane will just keep flying. Airliners that were taking off or landing and small aircraft (sport flyers, cropdusters, and the like) would be the ones in trouble.