A general method for directly measuring the low-frequency flux noise (below 10 Hz) in compound Josephson junction superconducting flux qubits has been used to study a series of 85 devices of varying design. The variation in flux noise across sets of qubits with identical designs was observed to be small. However, the levels of flux noise systematically varied between qubit designs with strong dependence upon qubit wiring length and wiring width. Furthermore, qubits fabricated above a superconducting ground plane yielded lower noise than qubits without such a layer. These results support the hypothesis that localized magnetic impurities in the vicinity of the qubit wiring are a key source of low frequency flux noise in superconducting devices.