OK, so Jason doesn't exactly pull off "sympathetic" so much as "Donnie Wahlberg's character in The Sixth Sense, as played by Crispin Glover." But you'd probably look a little washed out, too, if your Dad was using your brain to kill an entire race of people just because they remind him of you. Jason is a character who is built to be pitied, not hated. He's no more responsible for his actions than Master Chief is responsible for having worse aim when you're drunk.
As the climax closes in, Jason's dad is using his brain to trick Professor X into killing all the world's mutants. The X-Men figure out what's going on just in time, and Nightcrawler teleports to Professor X's side to find him sitting across from Jason in the belly of a crumbling dam.
"Thank goodness for the Protagonists With Disabilities Act, eh?"
Unfortunately for Jason, the dam is about to disintegrate and kill everyone in its general vicinity, he's in a wheelchair and he's spent the last hour helping his dad screw with the only people who could save him. Fortunately for Jason, there's a clear precedent for this sort of scenario that says you always take pity on the pathetic bad guy who's being taken advantage of. If you've seen The Goonies take pity on Sloth or The Karate Kid take mercy on Johnny Lawrence, you know that Nightcrawler's next move should be to lift Jason out of his wheelchair and tell him "It's not your fault" while a bear hug teleports them both to safety.
So what does Nightcrawler do?
Guys? Guys, it's not funny anymore.
Either because they forget that Jason is handicapped and therefore can't escape or even move, or because they just don't care, they just leave Jason to helplessly sit there as the entire dam collapses in on him.
It's not like they didn't have the time. A few minutes later, the X-Men are still escaping, and they take the time to offer to save the life of Jason's father -- the guy who was manipulating the mutant they just left to die. When Stryker tells them to go screw themselves, they just move on. The movie remembers to apply its core message of compassion for mutants and mankind to every single character except the most pathetic and helpless of them all.
But to be fair, he did have stupid hair, and he deserved to die for that.