We present a rigorous study on the impact of atmospheric molecular absorption on the linear propagation of ultrashort pulses in the mid-infrared wavelength region. An ultrafast thulium-based fiber laser was employed to experimentally investigate ultrashort-pulse propagation through the atmosphere in a spectral region containing several strong molecular absorption lines. The atmospheric absorption profile causes a significant degradation of the pulse quality in the time domain as well as a distortion of the transverse beam profile in the spatial domain. Numerical simulations carried out in the small signal limit accurately reproduce the experimental observations in the time domain and reveal that the relative loss in peak power after propagation can be more than twice as high as the relative amount of absorbed average power. Although their nature is purely linear (i.e. the intensities considered are sufficiently low) the discussed effects represent significant challenges to performance-scaling of mid-infrared ultrafast lasers operating in spectral regions with molecular absorption bands. Guidelines for an efficient mitigation of the pulse quality degradation and the beam profile distortion are discussed.