About 77% of the population is deficient in vitamin D.[0] You can't say "vitamins are bullshit" because only deficient people need them when a huge majority of the population IS deficient.
Sensible theory so then you need to run experiments to see if supplementing Vitamin D in "healthy" people actually improves their health outcomes. There are many reasons the theory might be wrong (ex. Natural variation of "normal" vitamin D levels). Unfortunately so far these studies have been mixed - even some negative outcomes.
From what I understand, the paper did a survey of Vitamin D related statistical studies. Then, went ahead and said that there existed a reverse causal link (Depression -> Stay Inside -> Low Vitamin D) as to why certain correlations existed. I am not going to make any judgements as to the causal conclusions they make. However, can you please clarify where you got the "negative outcomes"? There is no such thing mentioned in the NYT article, neither in the abstract of the Lancet paper.
The negative outcomes are not in those short summaries but the are easy to find. However just as a few positve studies don't prove Vitamin D is good for you a few negative studies don't prove it is bad. However negative studies do add to balance of evidence against use.
There is also the risk of overdose in any widely used supplement. Thankfully few of the 60,000 cases of vitamin toxicity in the US annually are Vitamin D (Iron is the riskyist).
A short walk in the sunlight is the best source of Vitamin D because your body naturally regulates it's production to near the optimum amount! I often wonder if the extreme avoidance of sunlight by some people is actually unhealthy...
[0] http://www.scientificamerican.com/article/vitamin-d-deficien...