Certified GKH Gardening Expert
They naturally grow a little bit above soil. When it is time to harvest, the shoulder should be protruding above soil. If yours are much more than that, it could be the soil is too warm for a cool season crop, or the soil is lacking in phosphorus or potassium which aids root development. Go ahead and harvest them when this happens. In the article below on fertilizing beets, you can see the top of the beet is above ground.
Here are more tips for growing beets:
https://www.gardeningknowhow.com/edible/vegetables/beets/growing-beets.htm
https://www.gardeningknowhow.com/edible/vegetables/beets/harvesting-beets.htm
https://www.gardeningknowhow.com/edible/vegetables/beets/fertilizing-beet-plants.htm