Honey is produced from nectar from clover by bees. As the clover does not need to be harvested to produce honey, the addition of a beehive to the farm is another way to increase profits. Each jar of honey produced also yields one XP.
Collecting jars of honey enable to earn Sweet as Honey ribbons.
Again the CL Devs are akin to the New Yorkers who firmly believed milk was made from a chemical added to water (the majority may have never seen a cow being milked) The bees collect nectar from flowering plants which they in turn convert the nectar into honey - see wikipedia:Nectar. The Pollen is collected by the bees by accident. It is not used to make honey, but when a bee takes pollen from one plant it then may transfer it to another and so on. In the process plants that have been pollinated will be able to reproduce . Bees also feed their developing young on Pollen and Honey. The Pollen brought back to their hives as a bonus. Bees love honey, they will go as far as stealing it from other bees.