For one small example, some years back, an office building had a natural gas leak, and at one point the roof blew off. (I was a witness.) The fire trucks came, the news choppers, and the reporters on the ground. That evening, I taped each of the local news broadcasts.
Every one of them got the fundamental facts wrong (such as calling the office building a warehouse), the timeline was wrong, etc. But those news reports are probably the only record of the event, and will go down in history as what happened.
Not that what happened there mattered, but it has made me suspicious of the veracity of news reports ever since. It doesn't even have to be malicious, the errors were just sloppy work in their desire to be done with it and move on to the next story.
I think the DNA work is interesting and somewhat more credible than purely physiological bone work, but I'd be skeptical to read into it too much. The article says they retrieved "1 to 2 million base pairs of ancient nuclear DNA" from fragments as small as 25-40 basepairs. Wikipedia tells me that humans have over 3 billion base pairs in their genome. Assuming the Sima hominid genome is somewhere within the same order of magnitude, they found less than 1% of the total genome. I'm not a geneticist, so I have no idea how they figured out how to piece those tiny fragments of 1% of the genome together in the right order, but it seems a thin branch to go out on to draw serious conclusions.
If we say that we can't know for sure and give up, then no advancements would ever be made in any field. On the other hand, we should recognize that science does not claim to provide us with certainty. Many of us speaking "objectively" with scientific "facts" often become emotional and arrogant when speaking to anyone who doesn't agree with our conclusions.