We use Molecular Dynamics simulations to determine the role that networks formed by fillers and polymers play in the rheology of polymer nanocomposites. We model the nano-filler particles as spherical particles in a matrix of unentangled polymer chains. We observe the effect of shear on the ability of the network to affect chain orientation. Our results indicate that above a critical concentration of filler particles, the network structure formed between the fillers and the polymers strongly affects the dynamics of the nanocomposite under shear. However, we also find that low concentrations of filler particles lead to a large increase in chain orientation (relative to the pure polymer case) when shear is applied. We suggest the mobility of the nano-filler particles helps in the construction and destruction of the networks seen in these melts. Our results indicate that the ability of fillers to maintain the network during shear results in the enhancement of the shear thinning effect at high concentrations of filler particles, while the ability of fillers to induce high degrees of orientation in polymer chains results in shear thinning being present even at lower concentrations of fillers.