Special conditions are required for organisms to be preserved and fossils to form, such as rapid burial in sediment, low levels of energy in the environment in which the organism died (high energy environments produce lots of fossil fragments as the organism gets broken up), and low levels of oxygen in the environment when the organism dies (the presence of oxygen encourages the breakdown of the organism due to bacterial decay).
Additionally, Earth movements due to tectonics, and other processes like metamorphism mean that many of the fossils are destroyed, as the rock they were formed in gets heated and compressed as more sediment accumulates on top.
