As the comments suggest, there probably is no one factor, but a big one seems to be the gas and ice giants took most of the carbon away.
In our Solar System as a whole, the primordial nebula had almost as much carbon as oxygen. However, during the accretion of the planets smaller objects, even including eventual neighborhood-clearing planets such as Earth, had only enough gravitational pull to retain nonvolatile substances. These include many oxides of elements such as alkali and alkaline earth metals, aluminum and silicon (lithophiles), not so many carbon-rich materials. Carbon remained largely as volatile compounds, mostly methane, and only the biggest objects at favorable positions were able to gather up these volatiles.
So a disproportionate amount of carbon ended up in the atmospheres of the giant planets instead of the solid structures of most everything else. Jupiter's atmosphere, for instance, has more carbon in the form of (predominantly) methane than oxygen in the form of (predominantly) water.