Wouldn't logic dictate that matter can't come from nothing.
No, it doesn't. That would be fallacy of composition (that a group will have the same properties as it components) - in other words just because everything in the universe has a cause and cannot create/destroy energy
1 would not imply that the universe itself has a cause or cannot have come from nothing (and vice-verse, doesn't imply it did either).
1 In fact neither of these things appear to be true, in QM things don't have causes and energy can be created and destroyed.