My guess is Alduin sensed a dragonborn in Helgen, but couldn't tell who it was, so he opted to just ry and kill them all. He wasn't focused on you specificly, presumably because he didn't know you were dragonborn.
That seems possible. Kind of funny then that Alduin unknowingly just signed his own fate by trying to get rid of the dragonborn. It at least shows the player has some backing from gods to be that lucky.
EDIT: Also it's a good point since at the beginning you don't even know your dragonborn and your power is very, very weak. I wouldn't be surprised if the more powerful you become the more chance there is a dragon will attack you, since it's much clearer to them that your character is the dovahkiin.