When you call plot on your graph or digraph object, specify the 'NodeColor' property. For example, here are two ways to create a digraph like the one in your example and plot it with node 1 being red and the others being green. I put each in their own figure window so you can compare the results.
d = digraph;
d = addedge(d, 1, 2:5);
You can explicitly specify a numnodes(d)-by-3 matrix of RGB values:
p = plot(d, 'NodeColor', [1 0 0; 0 1 0; 0 1 0; 0 1 0; 0 1 0]);
Or you can plot with all the nodes being the same color and highlight ones that are in some way 'special'.
h = plot(d, 'NodeColor', 'g');
highlight(h, 1, 'NodeColor', 'r');