Carbon is probably the single most versatile element in the universe in terms of the variety of chemical bonds it can make. This makes it the ideal element for being the basis of a highly complex system such as the chemistry of the human body. Carbon can form such a wide array or complex chemicals that it is perfect to use to make biomolecules such as sugars, starches, lipids (fats), nucleic acids (DNA), and proteins. The oxygen and hydrogen in the human body mostly originate from water and oxygen in the air because they are so abundant.
The Earth's crust contains large amounts of silicon, oxygen, and various metals. Carbon atoms present in the crust over time get broken down and oxidized by air to become gasses, particularly CO2 and hydrocarbons (methane, natural gas). That is why there is more carbon in the body than in the crust. Carbon tends to accumulate in biological molecules in the body while carbon in the Earth's crust tends to break down and be released to the atmosphere.