First up, you will need a much smaller step size to get an accurate solution using this explicit RK4 (with no error control). I suggest h = 0.05. Validate using say ode45 (which does have error control).
Then you will need to run your ode above three separate times, once starting from y(1) = 0.5, again with y(1) = 0.3, etc.
Then finally plot the result with plot(x,y,'o-').
x = 0:h:100;
Y = zeros(1,length(x));
y(1) = -0.5;
F_xy = @(t,r) 3.*exp(-t)-0.4*r;
k_1 = F_xy(x(i),y(i));
k_2 = F_xy(x(i)+0.5*h,y(i)+0.5*h*k_1);
k_3 = F_xy((x(i)+0.5*h),(y(i)+0.5*h*k_2));
k_4 = F_xy((x(i)+h),(y(i)+k_3*h));
y(i+1) = y(i) + (1/6)*(k_1+2*k_2+2*k_3+k_4)*h;
tspan = [0,100]; y0 = -0.5;
[tx, yx] = ode45(F_xy, tspan, y0)
plot(x,y,'o-', tx, yx, '--')