Carbon nanotubes (CNTs) have long been heralded as the material of choice for next-generation membranes. Some studies have suggested that boron nitride nanotubes (BNNTs) may offer higher transport of pure water than CNTs, while others conclude otherwise. In this work, we use a combination of simulations and experimental data to uncover the causes of this discrepancy and investigate the flow resistance through BNNT membranes in detail. By dividing the resistance of the nanotube membranes into their contributing components, we study the effects of pore end configuration, membrane length, and BNNT atom partial charges. Most molecular simulation studies of BNNT membranes use short membranes connected to high and low pressure reservoirs. Here we find that flow resistances in these short membranes are dominated by the resistance at the pore ends, which can obscure the understanding of water transport performance through the nanotubes and comparison between different nanotube materials. In contrast, it is the flow resistance inside the nanotubes that dominates microscale-thick laboratory membranes, and end resistances tend to be negligible. Judged by the nanotube flow resistance alone, we therefore find that CNTs are likely to consistently outperform BNNTs. Furthermore, we find a large role played by the choice of partial charges on the BN atoms in the flow resistance measurements in our molecular simulations. This paper highlights a way forward for comparing molecular simulations and experimental results.