We study the effect of proton irradiation on Ba(Fe0.96Co0.04)2As2 superconducting single crystals from combined magnetisation and magnetoresistivity measurements. The study allows the extraction of the values of the apparent pinning energy U0 of the samples prior to and after irradiation, as well as comparison of the values of U0 obtained from the flux-flow reversible region with those from the flux-creep irreversible region. Irradiation reduces Tc modestly, but significantly reduces U0 in both regimes: the critical current density Jc is modified, most strikingly by the disappearance of the second magnetisation peak after irradiation. Analysis of the functional form of the pinning force and of the temperature dependence of Jc for zero field, indicates that proton irradiation in this case has not changed the pinning regime, but has introduced a high density of shallow point-like defects. By considering a model that takes into account the effect of disorder on the irreversibility line, the data suggests that irradiation produced a considerable reduction in the average effective disorder overall, consistent with the changes observed in U0 and Jc.