Several reasons:

This article has picked a 200,000 colony increase in two years' time and decided to call it a "recovery". If, however, you look at the data overall since 1987, you can see that the trend is still downward — and that a 200,000 colony increase is merely a local maximum that happens to be barely better than a point twenty years previous. This local maximum might (can't do the math right now; on an iPad) just barely make an excursion outside one standard deviation from the mean. Look at their Y axis — those boxes are really thin and tall, disguising the slope of the decrease. That's dishonesty.

The best they can claim is that the rate of decline is decelerating a little.

Edit: oh, and their data is purely managed honeybee colonies. Perhaps they might have a different view if they had surveys of wild colonies as well.

Second, their sources for an opposing view to colony collapse syndrome in the article are economists critical of the beekeeping industry; this is like asking economists critical of the wind generation industry whether the science on anthropogenic climate change being driven by petroleum consumption, is valid.

TL;DR: article is not science and has no scientific sources; article's sources are economists.