I was wondering if its possible to get fliers not to crash when a unit stands on it... or is it hardcoded? I got the idea when i was playing the Dark Times online and i got in the holding compartment of the Rebel's transport, and it crashed the ship

It crashes the ship, not because you're in it, but because you are in it and the AI is piloting. It's not what you would call hardcoded either, but instead an artifact of the game because of how the AI is programed coupled with the way units move and are effected by moving objects around them.

No, a person is piloting, it was online

Nope, that can't be changed. It's just the way the game works. The only thing you can do to simulate something of the sort you suggested is to add an extra position where the player can stand or sit inside the vehicle, like in the Republic Gunship.

I did it with a person, and he didn't crash, I guess your person just stinks at flying.