Do the concepts of Newtonian and non-Newtonian fluids still hold at a nanoscopic level?
Generally Fick's laws of diffusion have been found to apply pretty well to molecular translational and rotational diffusion in solution. This means that we assume that the solvent is a continuous structureless fluid, which in practice means that the diffusing molecule should be far bigger than that of the solvent so that the solvent's molecular nature can be ignored. Surprisingly this works well with 'slip' and 'stick' boundary conditions down to situations where the solute is not that much bigger than the solvent, e.g.  rhodamine and similar dye molecules in solvents such as acetonitrile or ethanol. In your example of a protein in water then you might expect that it would behave 'normally' as just described.

However, in the cytoplasm the close packing of many similar sized and large molecules means that these can easily block the diffusion of any other (except for far, far smaller ones such as water) and so the situation is totally different and will be more like a percolation process where a slight reduction in packing can lead to a large, almost stepwise increase in diffusion coefficient. The idea of a single diffusion coefficient is therefore not helpful.