Aside from the bringing up kids issue, which is the biggest potential conflict, the next problem I see is if the Christian is on the more fundamental side, then they really believe that the atheist is destined for literal hell. So, if they're either going to try and eventually convert the atheist, or worse, they'll not let the discussion come up in the relationship, knowing that in their mind that person they supposedly love is doomed for eternal damnation. Now the atheist isn't worried about the actual fact of hell, but they should be worried about how devoted the Christian really is if they are comfortable with the notion.