The bees will eat the honey they have collected.
Well, actually it's a bit more complicated than that.
Bees collect nectar from flowers and make honey from it. Honey is what they eat, along with pollen, and bees need to store enough honey to feed themselves during the honey-gathering season, as well as during the winter months when the colony cannot go out to forage. So, when a beekeeper harvests honey from a hive, they are stealing the food the bees have worked hard to collect.
At first, that might sound cruel. However, fortunately for us, a healthy bee colony can collect more honey than it can consume on its own. A wise beekeeper will know how much honey the colony needs to survive and will only collect the excess for themselves. Furthermore, most of the honey harvesting takes place in midsummer so the bees have enough time to rebuild their honey stores.
But there's another reason to collect honey from the hive besides having something tasty to put on your toast. If the bees collect enough honey to completely fill the hive, two things can happen. First, the bees may decide their space is too small and swarm, leaving the hive in search of a larger home. The second thing that can happen is that the bees don't leave the hive but begin storing honey in the comb they usually use to raise young bees. This is also bad, as the colony won't be able to raise new bees. The bees and the colony will become very weak and may collapse as the existing bees age and die. Both situations are also bad for the beekeeper. A full hive of bees can represent an investment of several hundred dollars.
Therefore, don't feel bad about taking honey as long as you don't become too greedy. Always leave enough for your bees.