Can an imperfect hub make a disc rotor rub? I had a 160mm disc rotor on a road bike that was rubbing a bit in one spot, not severely, but enough for me to notice.  I've tried to true it a few times over the past couple months with little improvement.  I finally ordered a new rotor (sram centerline) and noticed it's also touching the pad, possibly more so than the old, but it sounds better under hard braking oddly enough.  I checked the new rotor before I put it on and it was straight.  I'm wondering if my hub is just imperfect and that's whats causing the alignment issue.  Is this common and if so is there a fix?
It could be a number of issues but I doubt you got a bad hub. Check to make sure your wheel is seated correctly in the fork. You could also try tightening/loosening the skewer to see if that may help align things. If all that doesn't work then you can try to realign the caliper if necessary. I wouldn't worry much if its just a little rub.