What does it mean if human DNA is in hot dogs?

There is definitely no food safety concern here. While the report you cite makes a big deal out of this, implying that there's some kind of serious problem being detected here, in their FAQ they say:

The most likely cause is hair, skin, or fingernail that was accidentally mixed in during the manufacturing process.

It is unlikely that human DNA is harmful to consumer health. In general, we consider human DNA a hygienic issue that degrades the quality of food more than a public health concern. Human DNA in products in our opinion speaks more issues [sic] of truth in advertising, pricing, and overall transparency.

What most people don't know us [sic] that some amounts of human DNA may fall within an acceptable regulatory range. That means that some human DNA is often allowed, regulatorily speaking. The amounts we detected in our research all fell within the acceptable regulatory range as we understand them.

It seems they're saying that this is all totally safe and allowed (by the people whose job it is to keep our food safe), and that the issue is one of transparency. I guess they think that food manufacturers should tell us that, as permitted by regulations, there are possibly tiny and completely safe amounts of human cells in food. But that seems pretty over-the-top; it's true about all food, so we'd have to slap that label on everything we eat.

Bottom line, food is not produced in a clean room environment. It's not a bunch of workers in bunny suits, being careful to not let a single skin cell float into the air and end up in your food; that'd be incredibly expensive and not provide any real benefit. So naturally, there's an opportunity for small amounts of human skin and hair to end up in your food.

And as Stephie pointed out, this is basically a DNA testing lab. Of course they have very sensitive equipment (which they also brag about in the FAQ), so they're able to detect things at a level that really shouldn't concern you. So as Lars also mentioned, it's kind of incredible that they were only able to find human DNA in 2% of samples. That means that 49/50 hot dogs are actually produced to a significantly higher standard than required!

Frankly, I think that report is presented fairly dishonestly. They deliberately neglected to mention in the initial results section that this is all safe, and instead implied that it was a problem you should worry about. Saying in the FAQ "What most people don't know..." hammers this home; they know that most people don't know this, and still didn't bother to say so.

Considering that food is not produced in a clean room environment, I'm surprised that it's only 2% of the samples. Humans are still involved in the production of food. The pig is turned into meat by humans. Humans clean machines. Humans take random samples from the production process. Humans put the ingredients for the sausage into a mixer. Humans stock the machines that will combine bread and sausage. Humans stock the machines that do the packaging.

And the person removing the Hot Dog from the package and doing a DNA test on it is also a human.