High school science classes teach us all about icebergs, or ice in general, and how the ice visible on the surface is only a small portion of the ice itself. This visual deception was one factor in the sinking of the Titanic in the early 20th century.
Figuratively, "the tip of the iceberg" is a small, visible portion of a larger, real problem.
Example: Company X is having trouble selling a particular product. A manager is examining customer complaints about the product. These complaints include frustration with customer support staff. The manager reports to the company president, "I'm sorry but, the complaints about thin-skinned customer support staff are just the tip of the iceberg. This product is the subject of five times the complaints of products we've sold in similar numbers. I'm convinced this is an indication of larger problems."