The accident was caused on purpose by the antagonists. It was set up for him to be transported, and while in route, the motocylist speed in and wrecked on purpose right in front of the van so that it would crash, thus, ideally, killing Lee Jun Ki's character. Except that he wasn't killed. He saw it right before it happened and already knew they were trying to kill him so in those precious few moments, he shielded himself from the flying glass with cloth. Due to his position in the van, he didn't take the brunt of the injuries and so was able to get away without a lot of injuries but for cuts and bruises.
Rewatch that whole scene again. :-) You can see what I'm talking about and it justifies why he's not overly injured. :-)