Non-equilibrium molecular dynamics simulations are widely employed to study transport fluid properties. Observables measured at the atomistic level can serve as inputs for continuum calculations, allowing for improved analysis of phenomena involving multiple scales. In hybrid modelling, uncertainties present in the information transferred across scales can have a significant impact on the final predictions. This work shows the influence of force-field variability on molecular measurements of the shear viscosity of water. In addition, the uncertainty propagation is demonstrated by quantifying the sensitivity of continuum velocity distribution to the particle-based calculations. The uncertainty is modelled with polynomial chaos expansion using a non-intrusive spectral projection strategy. The analysis confirms that low-order polynomial basis are sufficient to calculate the dispersion of observables.