Automatically plot different colored lines in MATLAB

You could use a colormap such as HSV to generate a set of colors. For example:

cc=hsv(12);
figure; 
hold on;
for i=1:12
    plot([0 1],[0 i],'color',cc(i,:));
end

MATLAB has 13 different named colormaps ('doc colormap' lists them all).
Another option for plotting lines in different colors is to use the LineStyleOrder property; see Defining the Color of Lines for Plotting in the MATLAB documentation for more information.
 

 

 

OR

 

 

Actually, a decent shortcut method for getting the colors to cycle is to use hold all; in place of hold on;. Each successive plot will rotate (automatically for you) through MATLAB's default colormap.
From the MATLAB site on hold:

hold all holds the plot and the current line color and line style so that subsequent plotting commands do not reset the ColorOrder and LineStyleOrder property values to the beginning of the list. Plotting commands continue cycling through the predefined colors and linestyles from where the last plot stopped in the list.