Although photosynthetic pigment-protein complexes are in noisy environments, recent experimental and theoretical results indicate that their excitation energy transfer (EET) can exhibit coherent characteristics for over hundreds of femtoseconds. Despite the almost universal observations of the coherence to some degree, questions still remain regarding the detailed role of the protein and the extent of high-temperature coherence. Here we adopt a theoretical method that incorporates an all-atom description of the photosynthetic complex within a semiclassical framework in order to study EET in the Fenna-Matthews-Olson complex. We observe that the vibrational modes of the chromophore tend to diminish the coherence at the ensemble level, yet much longer-lived coherences may be observed at the single-complex level. We also observe that coherent oscillations in the site populations also commence within tens of femtoseconds even when the system is initially prepared in a non-oscillatory stationary state. We show that the protein acts to maintain the electronic couplings among the system of embedded chromophores. We also investigate the extent to which the protein's electrostatic modulation that disperses the chromophore electronic energies may affect the coherence lifetime. Further, we observe that even though mutation-induced disruptions in the protein structure may change the coupling pattern, a relatively strong level of coupling and associated coherence in the dynamics still remain. Finally, we demonstrate that thermal fluctuations in the chromophore couplings induce some redundancy in the coherent energy-transfer pathway. Our results indicate that a description of both chromophore coupling strengths and their fluctuations is crucial to better understand coherent EET processes in photosynthetic systems.