First, you probably should move the plot functions outside the while loop. Build up the vectors, then plot!
But, the reason you are seeing only one line is that the two plots are plotting the same line. Below, I demonstrate this by changing the line specs (and moving the plot function outside the loop). You can see the first line plotted in red and the 2nd line plotted on top using a thick black dashed line.
t=0;
V = 0;
dt = 0.1;
S = 3;
CD = 0.1;
T = 10000;
m = 500;
plot(t,V)
hold on
while t<=5
t(end+1)=t(end)+dt;
F = T - CD*V(end)^21225*S/2;
V(end+1) = V(end) + dt*F/m;
end
plot(t,V, '-r')
while t <=10
t(end+1) = t(end)+dt;
F = T - CD*V(end)^21225*S/2;
V(end+1) = V(end) + dt*F/m;
end
plot(t,V, '--k', 'LineWidth', 5)
xlabel('Time (s)')
ylabel('Speed (m/s)')
title('Plot of speed against time')
