Well, my primary point is that the study does in fact mean something and the sample is reasonable. I don't have a lot of investment in the "why" part.
But you can continue your reasoning as long as you want, and end up never being able to say "why". Even if you have video of postal workers throwing away packages selectively, you never know why they did it.
Personally, I'm comfortable saying that this is a strong indication that some human beings somewhere mistreated packages because of the labels.
By the way, that does not mean that I think Christians (or any religious group) are more likely to do things like that than atheists.
I actually suspect (with the full understanding that these data do not say anything about this suspicion) that any package with a visible and potentially controversial label is more likely to get lost or delayed than a package without one. I would expect packages with tape with crosses, or stars of David, or "yay Obama", to get lost more than packages with no tape, because they will attract attention from random people who might dislike their messages. The control packages here had no tape at all.
I will admit that I would expect "atheist" packages to get lost more than "cross" packages, but that's just because there are more non-atheists than atheists, and therefore more chances for an "atheist" package to be handled by an anti-atheist person. If you equalized the numbers of atheists and Christians, you might get similar amounts of lossage for "cross" packages.