I was arguing over the math of this with my dad about this last night. Neither of us are Christian, by the way - we're more like die hard cynics.
The methodology used to calculate the probability that this Jesus son of Joseph was the Jesus son of Joseph and that this Maria was the Mary were a bit suspect.
Here's what they did: they calculated the probability that any random person of that time would be named "Yeshu Ben Yossef", and that any random person would be named "Mary". Same thing for Judah, Joseph, and Matthew. Then they multiplied those probabilities in order to find the conditional probability that all of those would be found together. They applied some further fuzz factors to calculate that the probability that this wasn't the actual Jesus and Mary was 1/600, or that there was a 599/600 chance that this actual was the holy family of Christianity.
What they didn't do was figure out that the chances that a couple would give a certain name to their children wasn't independent of their own names. Damn it, that didn't come out so clearly. Think about it this way: a parent will often not choose his child's name randomly (although the archeo/mathematicians assumed they did). A parent often chooses his child's name based on the names of their parents. My dad's name is P.... and he named me P.... My little sister's name is S...p... The names just sound better that way. Likewise, a person by the name of Joseph wouldn't choose his child's name randomly, he would be more likely to choose something that had a relationship to his own. Basically, this increases the probability that a particular set of names would be found together, and reduces the probability that this particular family found in the tomb was the holy family.
That's not even accounting for the mitochondrial DNA results, but then again, from what I've read, the mDNA doesn't provide a solid proof of anything - except that the contents of the "Jesus" tomb weren't related to the contents of the "Mary" tomb, but that the contents of the "Judah" tomb were related to the contents of both. So fine, you had some random couple named Jesus and Mary who had a son named Judah. But as the probability should show, that wasn't really that uncommon.