An option would be to choose a color based on magnitude first:
thisColor = whatever mapping you have between say mean(flow.Magnitude(:)) and your colormap
quiver(flow.Vx,flow.Vy, 'Color', thisColor)
PS: Just make sure quiver(flow.Vx, ...) gives you the same result as plot(flow), because I've always been confused by what's X and what's Y in these matrices, sometimes, due to the built-in functions in MATLAB being geared towards video applications, X direction can be top to bottom (rows of a matrix) and Y can be columns of the matrix meaning the horizontal axis! So if that's the case, you might find that quiver(flow.Vy, flow.Vx, ...) matches plot(flow) better.