3 reasons - much less likely to accidentally plug the jack into the wrong socket - whereas with the Vin header you could accidentally short the battery to ground by putting the wire in the wrong hole.
That would blow your fuse - you do have a fuse don't you? Large lead-acid batteries can source perhaps 1000A if shorted, a fuse is not a luxury.
The 4 reasons Amongst the reasons (nobody expects the Spanish Inquisition etc.) for using the barrel jack are the above 3, and the fact that a loose pin with +12v on it may short against something whereas the +12v connection in the barrel jack is shrouded.