Other important factors include the materials (concrete, steel, ...) and the type of design (ASD or LRFD) used to build the structure.
The type of criteria you said "cracks" will not be valid for a beam in a reinforced concrete structure. These beams crack because of concrete's low tensile strength, thus cracks are quite common and must be taken in consideration. Also, depending on the type of structure the materials may be stressed over their elastic region, which is true for reinforced concrete members in most of the current structures.
Another factor is design philosophy, what other posters explained above one method used to design. It's called Allowable/Permissible Stress Design which consists of calculating the stresses resulting from the service loads (expected loads), and a factor of safety is applied. The other philosophy is Limit state design or Load and resistance factor design. In this one, the adjusted resistances (depending on dimension of the structural member and the material's strength) are compared to the expected loads factored. The last method is used more widely around the world.
Addedum: Safety factors are a way to handle the "unknowns" like FredGarvin states. In fields like Geotechnical Engineering, they can be upto 45! if needed. In the cases of foundation on rocks, the uncertainty of the state of rock (cracked or not), the stresses acting on the rock before the structure and the other stratums surrounding the rock, plus others make it hard to trust the ultimate bearing capacity value obtained through the tests and theoretical equations.