Along the I24, I27, and I31 flybys of Io (1999-2001), the Energetic Particle Detector (EPD) onboard the Galileo spacecraft observed localized regions of energetic protons losses (155-1,250 keV). Using back-tracking particle simulations combined with a prescribed atmospheric distribution and a magnetohydrodynamics (MHD) model of the plasma/atmosphere interaction, we investigate the possible causes of these depletions. We focus on a limited region within two Io radii, which is dominated by Io's SO2 atmosphere. Our results show that charge exchange of protons with the SO2 atmosphere, absorption by the surface and the configuration of the electromagnetic field contribute to the observed proton depletion along the Galileo flybys. In the 155-240 keV energy range, charge exchange is either a major or the dominant loss process, depending on the flyby altitude. In the 540-1,250 keV range, as the charge exchange cross sections are small, the observed decrease of the proton flux is attributed to absorption by the surface and the perturbed electromagnetic fields, which divert the protons away from the detector. From a comparison between the modeled losses and the data we find indications of an extended atmosphere on the day/downstream side of Io, a lack of atmospheric collapse on the night/upstream side as well as a more global extended atmospheric component (>1 Io radius). Our results demonstrate that observations and modeling of proton depletion around the moon constitute an important tool to constrain the electromagnetic field configuration around Io and the radial and longitudinal atmospheric distribution, which is still poorly understood.