The story is partially true. A farm shed in Rasdorf, Hesse exploded on Monday, after probably an electric spark ignited a methane gas buildup. The original story appeared in many German publications as well, but contained very few details on the actual cause, e.g. Fuldaer Zeitung.
Today, the same paper printed a new article, stating that the methane buildup came from the manure and not directly from the flatulent cows: (translated from German)
The methane danger comes from the manure. The cows are not a risk.
The article goes on to explain that the shed is open to one side and should have been adequately ventilated. It is not clear how the methane concentration still could rise enough to produce an explosive mixture.
Still, looking at the relevant numbers, it does not seem unlikely that belching and farting cows alone can produce enough methane to create an explosive atmosphere. This report states that cows can emit 250-500 litres of methane daily. To keep the numbers simple (I know, there were only 90 cows in the shed, but assuming 100 makes it easier to calculate :-), 100 cows would each day emit 25-50m³ methan gas. Since a methane/air mixture is explosive at methane concentrations between 5 and 15%, the daily emissions of 100 cows would be enough to create 500 to 1000m³ of explosive methane/air. Since methane is much lighter than air, the required concentration would even be reached under the roof in a much larger room.
Edit: Oddthinking points out in his comment that sheds are ventilated. At least they should be. This German "Guidebook to air conditioning in sheds" from the Saxonian State Institute of Agriculture, states on page 7 that shed ventilation is in most cases regulated only by temperature, which may lead to high gas concentrations within the shed. It is not unlikely, that e.g. a low outdoor temperature may lead to insufficient ventilation in a shed, if the ventilation is merely controlled by air temperature and not any other parameters.