If your bees aren't working, the apiary should tell you what the problem is, in the top right corner of the GUI. Note that most bees are happy in a biome with normal temperature and humidity, such as a typical plains or forest, and need basic flowers- vanilla roses or dandelions work fine. For tropical bees, you'll need a warmer biome (such as a jungle) and vines nearby for flowers.
Also note that most bees (save Rocky, and all those derived from Rocky) won't work without direct sunlight on the apiary. There must be nothing above the apiary (save glass, torches, etc.), and it must be daytime and not raining. Rocky bees (and all the bees from ExtraBees that produce metals, gems, and the like) work pretty much anywhere, so long as there's stone nearby.